PubMed

On-line access to searching the Biomedical Literature

PubMed Tutorial

bull httpwwwnlmnihgovbsdpubmed_tutorialm1001html

bull This is an invaluable resource to learning to use this tool

bull You need to have the correct download for the interactive animations

NCBI Entrez

bull Common retrieval interface to many databases

bull Controlled links between databases

bull Maintained at the National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM)

Entrez 2004

PubMed vs Googlebull PubMed

ndash Peer reviewed journalsbull Multiple layers of quality

controlbull Edited and reviewed

text and grammar

ndash Combines automated and manual searching

ndash Structured links to other data sets (nucleic acid and protein sequences)

bull Googlendash The internet

bull Free but you get what you pay for

bull Variable document structure and grammar

ndash Fully automated search

ndash Unstructured links

Entrez PubMedbull Access

httpwwwncbinlmnihgoventrez bull Coverage

ndash Biomedical research broadlyndash Partial indexing of most recent couple months of journalsndash Lack of coverage in

bull CS and engineeringbull Physical chemistrybull Plant science

bull Searchable contentndash Free text search

bull title abstract indexing addressndash Controlled vocabulary

bull Mesh indexing journal dates substance names secondary indices

PubMed Tutorial

bull httpwwwnlmnihgovbsdpubmed_tutorialm1001html

bull This is an invaluable resource to learning to use this tool

bull You need to have the correct download for the interactive animations

NCBI Entrez

bull Common retrieval interface to many databases

bull Controlled links between databases

bull Maintained at the National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM)

Entrez 2004

PubMed vs Googlebull PubMed

ndash Peer reviewed journalsbull Multiple layers of quality

controlbull Edited and reviewed

text and grammar

ndash Combines automated and manual searching

ndash Structured links to other data sets (nucleic acid and protein sequences)

bull Googlendash The internet

bull Free but you get what you pay for

bull Variable document structure and grammar

ndash Fully automated search

ndash Unstructured links

Entrez PubMedbull Access

httpwwwncbinlmnihgoventrez bull Coverage

ndash Biomedical research broadlyndash Partial indexing of most recent couple months of journalsndash Lack of coverage in

bull CS and engineeringbull Physical chemistrybull Plant science

bull Searchable contentndash Free text search

bull title abstract indexing addressndash Controlled vocabulary

bull Mesh indexing journal dates substance names secondary indices

NCBI Entrez

bull Common retrieval interface to many databases

bull Controlled links between databases

bull Maintained at the National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM)

Entrez 2004

PubMed vs Googlebull PubMed

ndash Peer reviewed journalsbull Multiple layers of quality

controlbull Edited and reviewed

text and grammar

ndash Combines automated and manual searching

ndash Structured links to other data sets (nucleic acid and protein sequences)

bull Googlendash The internet

bull Free but you get what you pay for

bull Variable document structure and grammar

ndash Fully automated search

ndash Unstructured links

Entrez PubMedbull Access

httpwwwncbinlmnihgoventrez bull Coverage

ndash Biomedical research broadlyndash Partial indexing of most recent couple months of journalsndash Lack of coverage in

bull CS and engineeringbull Physical chemistrybull Plant science

bull Searchable contentndash Free text search

bull title abstract indexing addressndash Controlled vocabulary

bull Mesh indexing journal dates substance names secondary indices

PubMed vs Googlebull PubMed

ndash Peer reviewed journalsbull Multiple layers of quality

controlbull Edited and reviewed

text and grammar

ndash Combines automated and manual searching

ndash Structured links to other data sets (nucleic acid and protein sequences)

bull Googlendash The internet

bull Free but you get what you pay for

bull Variable document structure and grammar

ndash Fully automated search

ndash Unstructured links

Entrez PubMedbull Access

httpwwwncbinlmnihgoventrez bull Coverage

ndash Biomedical research broadlyndash Partial indexing of most recent couple months of journalsndash Lack of coverage in

bull CS and engineeringbull Physical chemistrybull Plant science

bull Searchable contentndash Free text search

bull title abstract indexing addressndash Controlled vocabulary

bull Mesh indexing journal dates substance names secondary indices

Entrez PubMedbull Access

httpwwwncbinlmnihgoventrez bull Coverage

ndash Biomedical research broadlyndash Partial indexing of most recent couple months of journalsndash Lack of coverage in

bull CS and engineeringbull Physical chemistrybull Plant science

bull Searchable contentndash Free text search

bull title abstract indexing addressndash Controlled vocabulary

bull Mesh indexing journal dates substance names secondary indices

Relationships between the Entrez primary information resources

Searching the Biomedical Literature

bull The PubMed literature is also in a flat file format with various fields

bull Knowledge of the fields in the file can allow you to focus your search and find what you are looking for more quickly

bull For example you can search by author and journal if you are looking for a specific personrsquos work and know where it was published

PubMed Search resultsbull Search results for

PubMed include the citation of the articles that your search has returned

bull Using Limits option you can search for ndash AuthorKeyword

Title Journalndash Language of pubndash Datendash Organism (human

or animal)ndash Sex (male or

female)ndash Type of publication

(Clinical Review Editorial etc)

PubMed Entrybull The

PubMed Entry includesndash Citationndash Link to

paper (maybe)

ndash Abstractndash PMIDndash UID

Uses and Limits of MeSH

Manually indexedndash Major topics =gt intelligent filteringndash Pick up things that are not in the titleabstractndash Takes time to add new headings (no MeSH headings

for most recent ~couple of months)ndash People are fallible so some misclassification occursndash Subheadings can be very useful but are less reliable

Strong medical biasndash Good for biomedical searchesndash Not as useful in technical areas agriculture and

plants

MeSH Vocabulary

bull The MeSH controlled vocabulary is a distinctive feature of MEDLINE

bull It imposes uniformity and consistency to the indexing of biomedical literature

bull MeSH terms are arranged in a hierarchical categorized system

bull These MeSH Tree Structures are updated annually

MeSH Homepage

bull httpwwwnlmnihgovmeshmeshhomehtml

bull MeSH is needed to help organize searching for efficiency

bull There are too many synonyms and abbreviations in the biomedical literature

bull Humans still help with the sorting of the headings This is called ldquocurationrdquo

Structure of MeSH

DivisionsAnatomy [A] Organisms [B] Diseases [C] Chemicals and Drugs [D] Analytical Diagnostic and Therapeutic

Techniques and Equipment [E] Psychiatry and Psychology [F] Biological Sciences [G] Physical Sciences [H] Anthropology Education Sociology and

Social Phenomena [I] Technology and Food and Beverages [J] Humanities [K] Information Science [L] Persons [M] Health Care [N] Geographic Locations [Z]

Hierarchy with Multiple Inheritance

Amino Acids Peptides and Proteins [D12] Proteins [D12776] DNA-Binding Proteins [D12776260] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Nuclear Proteins [D12776660] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Transcription Factors [D12776930] NF-kappa B [D12776260600]

Searching the Biomedical Literature

bull The PubMed literature is also in a flat file format with various fields

bull Knowledge of the fields in the file can allow you to focus your search and find what you are looking for more quickly

bull For example you can search by author and journal if you are looking for a specific personrsquos work and know where it was published

PubMed Search resultsbull Search results for

PubMed include the citation of the articles that your search has returned

bull Using Limits option you can search for ndash AuthorKeyword

Title Journalndash Language of pubndash Datendash Organism (human

or animal)ndash Sex (male or

female)ndash Type of publication

(Clinical Review Editorial etc)

PubMed Entrybull The

PubMed Entry includesndash Citationndash Link to

paper (maybe)

ndash Abstractndash PMIDndash UID

Uses and Limits of MeSH

Manually indexedndash Major topics =gt intelligent filteringndash Pick up things that are not in the titleabstractndash Takes time to add new headings (no MeSH headings

for most recent ~couple of months)ndash People are fallible so some misclassification occursndash Subheadings can be very useful but are less reliable

Strong medical biasndash Good for biomedical searchesndash Not as useful in technical areas agriculture and

plants

MeSH Vocabulary

bull The MeSH controlled vocabulary is a distinctive feature of MEDLINE

bull It imposes uniformity and consistency to the indexing of biomedical literature

bull MeSH terms are arranged in a hierarchical categorized system

bull These MeSH Tree Structures are updated annually

MeSH Homepage

bull httpwwwnlmnihgovmeshmeshhomehtml

bull MeSH is needed to help organize searching for efficiency

bull There are too many synonyms and abbreviations in the biomedical literature

bull Humans still help with the sorting of the headings This is called ldquocurationrdquo

Structure of MeSH

DivisionsAnatomy [A] Organisms [B] Diseases [C] Chemicals and Drugs [D] Analytical Diagnostic and Therapeutic

Techniques and Equipment [E] Psychiatry and Psychology [F] Biological Sciences [G] Physical Sciences [H] Anthropology Education Sociology and

Social Phenomena [I] Technology and Food and Beverages [J] Humanities [K] Information Science [L] Persons [M] Health Care [N] Geographic Locations [Z]

Hierarchy with Multiple Inheritance

Amino Acids Peptides and Proteins [D12] Proteins [D12776] DNA-Binding Proteins [D12776260] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Nuclear Proteins [D12776660] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Transcription Factors [D12776930] NF-kappa B [D12776260600]

PubMed Search resultsbull Search results for

PubMed include the citation of the articles that your search has returned

bull Using Limits option you can search for ndash AuthorKeyword

Title Journalndash Language of pubndash Datendash Organism (human

or animal)ndash Sex (male or

female)ndash Type of publication

(Clinical Review Editorial etc)

PubMed Entrybull The

PubMed Entry includesndash Citationndash Link to

paper (maybe)

ndash Abstractndash PMIDndash UID

Uses and Limits of MeSH

Manually indexedndash Major topics =gt intelligent filteringndash Pick up things that are not in the titleabstractndash Takes time to add new headings (no MeSH headings

for most recent ~couple of months)ndash People are fallible so some misclassification occursndash Subheadings can be very useful but are less reliable

Strong medical biasndash Good for biomedical searchesndash Not as useful in technical areas agriculture and

plants

MeSH Vocabulary

bull The MeSH controlled vocabulary is a distinctive feature of MEDLINE

bull It imposes uniformity and consistency to the indexing of biomedical literature

bull MeSH terms are arranged in a hierarchical categorized system

bull These MeSH Tree Structures are updated annually

MeSH Homepage

bull httpwwwnlmnihgovmeshmeshhomehtml

bull MeSH is needed to help organize searching for efficiency

bull There are too many synonyms and abbreviations in the biomedical literature

bull Humans still help with the sorting of the headings This is called ldquocurationrdquo

Structure of MeSH

DivisionsAnatomy [A] Organisms [B] Diseases [C] Chemicals and Drugs [D] Analytical Diagnostic and Therapeutic

Techniques and Equipment [E] Psychiatry and Psychology [F] Biological Sciences [G] Physical Sciences [H] Anthropology Education Sociology and

Social Phenomena [I] Technology and Food and Beverages [J] Humanities [K] Information Science [L] Persons [M] Health Care [N] Geographic Locations [Z]

Hierarchy with Multiple Inheritance

Amino Acids Peptides and Proteins [D12] Proteins [D12776] DNA-Binding Proteins [D12776260] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Nuclear Proteins [D12776660] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Transcription Factors [D12776930] NF-kappa B [D12776260600]

PubMed Entrybull The

PubMed Entry includesndash Citationndash Link to

paper (maybe)

ndash Abstractndash PMIDndash UID

Uses and Limits of MeSH

Manually indexedndash Major topics =gt intelligent filteringndash Pick up things that are not in the titleabstractndash Takes time to add new headings (no MeSH headings

for most recent ~couple of months)ndash People are fallible so some misclassification occursndash Subheadings can be very useful but are less reliable

Strong medical biasndash Good for biomedical searchesndash Not as useful in technical areas agriculture and

plants

MeSH Vocabulary

bull The MeSH controlled vocabulary is a distinctive feature of MEDLINE

bull It imposes uniformity and consistency to the indexing of biomedical literature

bull MeSH terms are arranged in a hierarchical categorized system

bull These MeSH Tree Structures are updated annually

MeSH Homepage

bull httpwwwnlmnihgovmeshmeshhomehtml

bull MeSH is needed to help organize searching for efficiency

bull There are too many synonyms and abbreviations in the biomedical literature

bull Humans still help with the sorting of the headings This is called ldquocurationrdquo

Structure of MeSH

DivisionsAnatomy [A] Organisms [B] Diseases [C] Chemicals and Drugs [D] Analytical Diagnostic and Therapeutic

Techniques and Equipment [E] Psychiatry and Psychology [F] Biological Sciences [G] Physical Sciences [H] Anthropology Education Sociology and

Social Phenomena [I] Technology and Food and Beverages [J] Humanities [K] Information Science [L] Persons [M] Health Care [N] Geographic Locations [Z]

Hierarchy with Multiple Inheritance

Amino Acids Peptides and Proteins [D12] Proteins [D12776] DNA-Binding Proteins [D12776260] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Nuclear Proteins [D12776660] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Transcription Factors [D12776930] NF-kappa B [D12776260600]

Uses and Limits of MeSH

Manually indexedndash Major topics =gt intelligent filteringndash Pick up things that are not in the titleabstractndash Takes time to add new headings (no MeSH headings

for most recent ~couple of months)ndash People are fallible so some misclassification occursndash Subheadings can be very useful but are less reliable

Strong medical biasndash Good for biomedical searchesndash Not as useful in technical areas agriculture and

plants

MeSH Vocabulary

bull The MeSH controlled vocabulary is a distinctive feature of MEDLINE

bull It imposes uniformity and consistency to the indexing of biomedical literature

bull MeSH terms are arranged in a hierarchical categorized system

bull These MeSH Tree Structures are updated annually

MeSH Homepage

bull httpwwwnlmnihgovmeshmeshhomehtml

bull MeSH is needed to help organize searching for efficiency

bull There are too many synonyms and abbreviations in the biomedical literature

bull Humans still help with the sorting of the headings This is called ldquocurationrdquo

Structure of MeSH

DivisionsAnatomy [A] Organisms [B] Diseases [C] Chemicals and Drugs [D] Analytical Diagnostic and Therapeutic

Techniques and Equipment [E] Psychiatry and Psychology [F] Biological Sciences [G] Physical Sciences [H] Anthropology Education Sociology and

Social Phenomena [I] Technology and Food and Beverages [J] Humanities [K] Information Science [L] Persons [M] Health Care [N] Geographic Locations [Z]

Hierarchy with Multiple Inheritance

Amino Acids Peptides and Proteins [D12] Proteins [D12776] DNA-Binding Proteins [D12776260] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Nuclear Proteins [D12776660] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Transcription Factors [D12776930] NF-kappa B [D12776260600]

MeSH Vocabulary

bull The MeSH controlled vocabulary is a distinctive feature of MEDLINE

bull It imposes uniformity and consistency to the indexing of biomedical literature

bull MeSH terms are arranged in a hierarchical categorized system

bull These MeSH Tree Structures are updated annually

MeSH Homepage

bull httpwwwnlmnihgovmeshmeshhomehtml

bull MeSH is needed to help organize searching for efficiency

bull There are too many synonyms and abbreviations in the biomedical literature

bull Humans still help with the sorting of the headings This is called ldquocurationrdquo

Structure of MeSH

DivisionsAnatomy [A] Organisms [B] Diseases [C] Chemicals and Drugs [D] Analytical Diagnostic and Therapeutic

Techniques and Equipment [E] Psychiatry and Psychology [F] Biological Sciences [G] Physical Sciences [H] Anthropology Education Sociology and

Social Phenomena [I] Technology and Food and Beverages [J] Humanities [K] Information Science [L] Persons [M] Health Care [N] Geographic Locations [Z]

Hierarchy with Multiple Inheritance

Amino Acids Peptides and Proteins [D12] Proteins [D12776] DNA-Binding Proteins [D12776260] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Nuclear Proteins [D12776660] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Transcription Factors [D12776930] NF-kappa B [D12776260600]

MeSH Homepage

bull httpwwwnlmnihgovmeshmeshhomehtml

bull MeSH is needed to help organize searching for efficiency

bull There are too many synonyms and abbreviations in the biomedical literature

bull Humans still help with the sorting of the headings This is called ldquocurationrdquo

Structure of MeSH

DivisionsAnatomy [A] Organisms [B] Diseases [C] Chemicals and Drugs [D] Analytical Diagnostic and Therapeutic

Techniques and Equipment [E] Psychiatry and Psychology [F] Biological Sciences [G] Physical Sciences [H] Anthropology Education Sociology and

Social Phenomena [I] Technology and Food and Beverages [J] Humanities [K] Information Science [L] Persons [M] Health Care [N] Geographic Locations [Z]

Hierarchy with Multiple Inheritance

Amino Acids Peptides and Proteins [D12] Proteins [D12776] DNA-Binding Proteins [D12776260] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Nuclear Proteins [D12776660] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Transcription Factors [D12776930] NF-kappa B [D12776260600]

Structure of MeSH

DivisionsAnatomy [A] Organisms [B] Diseases [C] Chemicals and Drugs [D] Analytical Diagnostic and Therapeutic

Techniques and Equipment [E] Psychiatry and Psychology [F] Biological Sciences [G] Physical Sciences [H] Anthropology Education Sociology and

Social Phenomena [I] Technology and Food and Beverages [J] Humanities [K] Information Science [L] Persons [M] Health Care [N] Geographic Locations [Z]

Hierarchy with Multiple Inheritance

Amino Acids Peptides and Proteins [D12] Proteins [D12776] DNA-Binding Proteins [D12776260] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Nuclear Proteins [D12776660] NF-kappa B [D12776260600]

Amino Acids Peptides and Proteins [D12] Proteins [D12776] Transcription Factors [D12776930] NF-kappa B [D12776260600]

MeSH Full ListingNF-kappa B

Ubiquitous inducible nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits NF-kappa B1 and relA

Year introduced 1991Ssubheadings

administration and dosage agonists analysis antagonists and inhibitors biosynthesis blood cerebrospinal fluid chemistry classification deficiency diagnostic use drug effects genetics immunology isolation and purification metabolism pharmacokinetics pharmacology physiology radiation effects secretion therapeutic use toxicity ultrastructure

Restrict Search to Major Topic headings only Do Not Explode this term

(ie do not include MeSH terms found below this term in the MeSH tree)

Entry Terms NF-kB NF kB Nuclear Factor kappa B kappa B Enhancer Binding Protein Immunoglobulin Enhancer-Binding Protein Enhancer-Binding Protein Immunoglobulin Immunoglobulin Enhancer Binding Protein Transcription Factor NF-kB Factor NF-kB Transcription NF-kB Transcription Factor Transcription Factor NF kB Ig-EBP-1 Ig EBP 1

Previous Indexing DNA-Binding Proteins (1987-1990) Transcription Factors (1987-1990)

See Also I-kappa B

All MeSH Categories Chemicals and Drugs Category Amino Acids Peptides and Proteins Proteins DNA-Binding Proteins NF-kappa B

All MeSH Categories Chemicals and Drugs Category Amino Acids Peptides and Proteins Proteins Nuclear Proteins NF-kappa B

All MeSH Categories Chemicals and Drugs Category Amino Acids Peptides and Proteins Proteins Transcription Factors NF-kappa B

Journals Database

Entrez -gt JournalsA database of journal names and informationEntry structure

Nature genetics pISSN 1061-4036MEDLINE Abbr Nat GenetISO Abbr Nat GenetNLM ID 9216904

bull See also ISI databases

Boolean Logic

bull Boolean logic symbolically represents relationships between entities There are three Boolean operators

bull ANDndash Use the AND operator to retrieve a set in

which each citation contains ALL the search terms This operator places no condition on where the terms are found in relation to one another the terms simply have to appear somewhere in the same citation

Boolean Logic

bull ORndash Use the OR operator to retrieve documents

that contain at least one of the specified search terms

ndash Use OR when you want to pull together articles on similar subjects

bull NOTndash Use the NOT operator to exclude the

retrieval of terms from your search ndash Be careful with NOT as you can exclude

things you might want

Boolean Logic in PubMed

bull Boolean operators -- AND OR NOT -- must be entered in uppercase letters

bull Boolean operators are processed from left to right

bull Use parentheses to nest terms together so they will be processed as a unit and then incorporated into the overall strategy

Boolean Logic in PubMed

Boolean Logic is revealed by clicking Details

bull Entrez attempts to intelligently parse your queryQuery dna binding transcription factor macrophageDetails =gt ((((dna[MeSH Terms] OR dna[Text Word]) AND

((pharmacokinetics[MeSH Subheading] OR pharmacokineticsldquo [MeSH Terms]) OR binding [Text Word])) AND (transcription factorsldquo [MeSH Terms] OR transcription factor [Text Word])) AND (macrophages[MeSH Terms] OR macrophage [Text Word]))

bull You can force a Boolean searchQuery ldquodna bindingrdquo AND ldquotranscription factorrdquo AND

macrophageDetails =gt ((dna binding[All Fields] AND transcription

factor[All Fields]) AND (macrophages[MeSH Terms] OR macrophage[Text Word]))

Phrase Searching

bull Specify with quotesldquotranscription factorrdquo vs ldquotranscriptionrdquo

ldquofactorrdquo

bull Precomputedndash Fastndash Often mapped to synonyms and MeSH

termsndash Just because you get a ldquophrase not foundrdquo

message does not mean it is not present

Text Neighboring

Related articles link (single or multiple articles)ndash Term usage similarity

bull Articles talking about the same thing are likely to use the same words

ndash Good recall (sensitivity)ndash Precomputed and fast

Limitationsndash Strictly algorithmic no understanding

bull ldquoRas activates PI3Krdquo vs ldquoPI3K activates Rasrdquondash Historical and author biases in vocabularyndash Poor precision (specificity)ndash Ranking can not satisfy everyone

Computational Issues in Statistical Text Retrieval

bull Stop wordsndash Simple words like ldquotherdquo and ldquoandrdquo are not worth scoring

bull Term weightsndash We should weight matches of rare words more heavily than

matches of common wordsbull Stemming and synonyms

ndash Need to stem verbs and plural formsndash May or may not be able to reduce to a normalized set of

synonymsbull Normalizing for length

ndash Donrsquot want to exclude short articles or articles without an abstract

bull All vs all comparison is not feasiblendash 107 articles =gt 1014 comparisons not feasiblendash Compute demands of the task are growing faster than Moorersquos

law

Entrez Clipboard

bull The Clipboard gives you a place to collect selected citations from one search or several searches

bull After you add citations to the Clipboard you may then want to use the print save or order buttons

bull The maximum number of items that can be placed in the Clipboard is 500

bull Once you have added items to the Clipboard you can click on Clipboard from the Features bar to view your selections

bull PubMed Central uses cookies to add your selections to the Clipboard To use this feature your web browser must be set to accept cookies

Using Clipboard

bull Add to Clipboard ndash To place an item in the Clipboard click on the

check box to the left of the citationndash Select Clipboard from the Send to pull-down

menundash Then click the Send to button Once you have

added a citation to the Clipboard the record number color will change to green Send to ldquoclipboardrdquo

ndash You can save results collected from multiple searches

ndash The Clipboard will hold a maximum of 500 itemsndash Clipboard items will be lost after 1 hours of

inactivity

Saving from the Clipboard

bull Citations are initially displayed in the summary format in the relevancy order

bull Use Sort to change the order You can select all or individual citations to display or save in one of the citation display formats

bull Select the desired format from the pull-down menu click Save to save your selections to a file or use the Print feature of your web browser to print the citations

bull Printing from your web browser will only print the information and citations listed on the web page

bull You may also display citations as plain text without the sidebar menu and toolbars by clicking the Text button

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Boolean Logic

bull Boolean logic symbolically represents relationships between entities There are three Boolean operators

bull ANDndash Use the AND operator to retrieve a set in

which each citation contains ALL the search terms This operator places no condition on where the terms are found in relation to one another the terms simply have to appear somewhere in the same citation

Boolean Logic

bull ORndash Use the OR operator to retrieve documents

that contain at least one of the specified search terms

ndash Use OR when you want to pull together articles on similar subjects

bull NOTndash Use the NOT operator to exclude the

retrieval of terms from your search ndash Be careful with NOT as you can exclude

things you might want

Boolean Logic in PubMed

bull Boolean operators -- AND OR NOT -- must be entered in uppercase letters

bull Boolean operators are processed from left to right

bull Use parentheses to nest terms together so they will be processed as a unit and then incorporated into the overall strategy

Boolean Logic in PubMed

Boolean Logic is revealed by clicking Details

bull Entrez attempts to intelligently parse your queryQuery dna binding transcription factor macrophageDetails =gt ((((dna[MeSH Terms] OR dna[Text Word]) AND

((pharmacokinetics[MeSH Subheading] OR pharmacokineticsldquo [MeSH Terms]) OR binding [Text Word])) AND (transcription factorsldquo [MeSH Terms] OR transcription factor [Text Word])) AND (macrophages[MeSH Terms] OR macrophage [Text Word]))

bull You can force a Boolean searchQuery ldquodna bindingrdquo AND ldquotranscription factorrdquo AND

macrophageDetails =gt ((dna binding[All Fields] AND transcription

factor[All Fields]) AND (macrophages[MeSH Terms] OR macrophage[Text Word]))

Phrase Searching

bull Specify with quotesldquotranscription factorrdquo vs ldquotranscriptionrdquo

ldquofactorrdquo

bull Precomputedndash Fastndash Often mapped to synonyms and MeSH

termsndash Just because you get a ldquophrase not foundrdquo

message does not mean it is not present

Text Neighboring

Related articles link (single or multiple articles)ndash Term usage similarity

bull Articles talking about the same thing are likely to use the same words

ndash Good recall (sensitivity)ndash Precomputed and fast

Limitationsndash Strictly algorithmic no understanding

bull ldquoRas activates PI3Krdquo vs ldquoPI3K activates Rasrdquondash Historical and author biases in vocabularyndash Poor precision (specificity)ndash Ranking can not satisfy everyone

Computational Issues in Statistical Text Retrieval

bull Stop wordsndash Simple words like ldquotherdquo and ldquoandrdquo are not worth scoring

bull Term weightsndash We should weight matches of rare words more heavily than

matches of common wordsbull Stemming and synonyms

ndash Need to stem verbs and plural formsndash May or may not be able to reduce to a normalized set of

synonymsbull Normalizing for length

ndash Donrsquot want to exclude short articles or articles without an abstract

bull All vs all comparison is not feasiblendash 107 articles =gt 1014 comparisons not feasiblendash Compute demands of the task are growing faster than Moorersquos

law

Entrez Clipboard

bull The Clipboard gives you a place to collect selected citations from one search or several searches

bull After you add citations to the Clipboard you may then want to use the print save or order buttons

bull The maximum number of items that can be placed in the Clipboard is 500

bull Once you have added items to the Clipboard you can click on Clipboard from the Features bar to view your selections

bull PubMed Central uses cookies to add your selections to the Clipboard To use this feature your web browser must be set to accept cookies

Using Clipboard

bull Add to Clipboard ndash To place an item in the Clipboard click on the

check box to the left of the citationndash Select Clipboard from the Send to pull-down

menundash Then click the Send to button Once you have

added a citation to the Clipboard the record number color will change to green Send to ldquoclipboardrdquo

ndash You can save results collected from multiple searches

ndash The Clipboard will hold a maximum of 500 itemsndash Clipboard items will be lost after 1 hours of

inactivity

Saving from the Clipboard

bull Citations are initially displayed in the summary format in the relevancy order

bull Use Sort to change the order You can select all or individual citations to display or save in one of the citation display formats

bull Select the desired format from the pull-down menu click Save to save your selections to a file or use the Print feature of your web browser to print the citations

bull Printing from your web browser will only print the information and citations listed on the web page

bull You may also display citations as plain text without the sidebar menu and toolbars by clicking the Text button

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Boolean Logic

bull ORndash Use the OR operator to retrieve documents

that contain at least one of the specified search terms

ndash Use OR when you want to pull together articles on similar subjects

bull NOTndash Use the NOT operator to exclude the

retrieval of terms from your search ndash Be careful with NOT as you can exclude

things you might want

Boolean Logic in PubMed

bull Boolean operators -- AND OR NOT -- must be entered in uppercase letters

bull Boolean operators are processed from left to right

bull Use parentheses to nest terms together so they will be processed as a unit and then incorporated into the overall strategy

Boolean Logic in PubMed

Boolean Logic is revealed by clicking Details

bull Entrez attempts to intelligently parse your queryQuery dna binding transcription factor macrophageDetails =gt ((((dna[MeSH Terms] OR dna[Text Word]) AND

((pharmacokinetics[MeSH Subheading] OR pharmacokineticsldquo [MeSH Terms]) OR binding [Text Word])) AND (transcription factorsldquo [MeSH Terms] OR transcription factor [Text Word])) AND (macrophages[MeSH Terms] OR macrophage [Text Word]))

bull You can force a Boolean searchQuery ldquodna bindingrdquo AND ldquotranscription factorrdquo AND

macrophageDetails =gt ((dna binding[All Fields] AND transcription

factor[All Fields]) AND (macrophages[MeSH Terms] OR macrophage[Text Word]))

Phrase Searching

bull Specify with quotesldquotranscription factorrdquo vs ldquotranscriptionrdquo

ldquofactorrdquo

bull Precomputedndash Fastndash Often mapped to synonyms and MeSH

termsndash Just because you get a ldquophrase not foundrdquo

message does not mean it is not present

Text Neighboring

Related articles link (single or multiple articles)ndash Term usage similarity

bull Articles talking about the same thing are likely to use the same words

ndash Good recall (sensitivity)ndash Precomputed and fast

Limitationsndash Strictly algorithmic no understanding

bull ldquoRas activates PI3Krdquo vs ldquoPI3K activates Rasrdquondash Historical and author biases in vocabularyndash Poor precision (specificity)ndash Ranking can not satisfy everyone

Computational Issues in Statistical Text Retrieval

bull Stop wordsndash Simple words like ldquotherdquo and ldquoandrdquo are not worth scoring

bull Term weightsndash We should weight matches of rare words more heavily than

matches of common wordsbull Stemming and synonyms

ndash Need to stem verbs and plural formsndash May or may not be able to reduce to a normalized set of

synonymsbull Normalizing for length

ndash Donrsquot want to exclude short articles or articles without an abstract

bull All vs all comparison is not feasiblendash 107 articles =gt 1014 comparisons not feasiblendash Compute demands of the task are growing faster than Moorersquos

law

Entrez Clipboard

bull The Clipboard gives you a place to collect selected citations from one search or several searches

bull After you add citations to the Clipboard you may then want to use the print save or order buttons

bull The maximum number of items that can be placed in the Clipboard is 500

bull Once you have added items to the Clipboard you can click on Clipboard from the Features bar to view your selections

bull PubMed Central uses cookies to add your selections to the Clipboard To use this feature your web browser must be set to accept cookies

Using Clipboard

bull Add to Clipboard ndash To place an item in the Clipboard click on the

check box to the left of the citationndash Select Clipboard from the Send to pull-down

menundash Then click the Send to button Once you have

added a citation to the Clipboard the record number color will change to green Send to ldquoclipboardrdquo

ndash You can save results collected from multiple searches

ndash The Clipboard will hold a maximum of 500 itemsndash Clipboard items will be lost after 1 hours of

inactivity

Saving from the Clipboard

bull Citations are initially displayed in the summary format in the relevancy order

bull Use Sort to change the order You can select all or individual citations to display or save in one of the citation display formats

bull Select the desired format from the pull-down menu click Save to save your selections to a file or use the Print feature of your web browser to print the citations

bull Printing from your web browser will only print the information and citations listed on the web page

bull You may also display citations as plain text without the sidebar menu and toolbars by clicking the Text button

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Boolean Logic in PubMed

bull Boolean operators -- AND OR NOT -- must be entered in uppercase letters

bull Boolean operators are processed from left to right

bull Use parentheses to nest terms together so they will be processed as a unit and then incorporated into the overall strategy

Boolean Logic in PubMed

Boolean Logic is revealed by clicking Details

bull Entrez attempts to intelligently parse your queryQuery dna binding transcription factor macrophageDetails =gt ((((dna[MeSH Terms] OR dna[Text Word]) AND

((pharmacokinetics[MeSH Subheading] OR pharmacokineticsldquo [MeSH Terms]) OR binding [Text Word])) AND (transcription factorsldquo [MeSH Terms] OR transcription factor [Text Word])) AND (macrophages[MeSH Terms] OR macrophage [Text Word]))

bull You can force a Boolean searchQuery ldquodna bindingrdquo AND ldquotranscription factorrdquo AND

macrophageDetails =gt ((dna binding[All Fields] AND transcription

factor[All Fields]) AND (macrophages[MeSH Terms] OR macrophage[Text Word]))

Phrase Searching

bull Specify with quotesldquotranscription factorrdquo vs ldquotranscriptionrdquo

ldquofactorrdquo

bull Precomputedndash Fastndash Often mapped to synonyms and MeSH

termsndash Just because you get a ldquophrase not foundrdquo

message does not mean it is not present

Text Neighboring

Related articles link (single or multiple articles)ndash Term usage similarity

bull Articles talking about the same thing are likely to use the same words

ndash Good recall (sensitivity)ndash Precomputed and fast

Limitationsndash Strictly algorithmic no understanding

bull ldquoRas activates PI3Krdquo vs ldquoPI3K activates Rasrdquondash Historical and author biases in vocabularyndash Poor precision (specificity)ndash Ranking can not satisfy everyone

Computational Issues in Statistical Text Retrieval

bull Stop wordsndash Simple words like ldquotherdquo and ldquoandrdquo are not worth scoring

bull Term weightsndash We should weight matches of rare words more heavily than

matches of common wordsbull Stemming and synonyms

ndash Need to stem verbs and plural formsndash May or may not be able to reduce to a normalized set of

synonymsbull Normalizing for length

ndash Donrsquot want to exclude short articles or articles without an abstract

bull All vs all comparison is not feasiblendash 107 articles =gt 1014 comparisons not feasiblendash Compute demands of the task are growing faster than Moorersquos

law

Entrez Clipboard

bull The Clipboard gives you a place to collect selected citations from one search or several searches

bull After you add citations to the Clipboard you may then want to use the print save or order buttons

bull The maximum number of items that can be placed in the Clipboard is 500

bull Once you have added items to the Clipboard you can click on Clipboard from the Features bar to view your selections

bull PubMed Central uses cookies to add your selections to the Clipboard To use this feature your web browser must be set to accept cookies

Using Clipboard

bull Add to Clipboard ndash To place an item in the Clipboard click on the

check box to the left of the citationndash Select Clipboard from the Send to pull-down

menundash Then click the Send to button Once you have

added a citation to the Clipboard the record number color will change to green Send to ldquoclipboardrdquo

ndash You can save results collected from multiple searches

ndash The Clipboard will hold a maximum of 500 itemsndash Clipboard items will be lost after 1 hours of

inactivity

Saving from the Clipboard

bull Citations are initially displayed in the summary format in the relevancy order

bull Use Sort to change the order You can select all or individual citations to display or save in one of the citation display formats

bull Select the desired format from the pull-down menu click Save to save your selections to a file or use the Print feature of your web browser to print the citations

bull Printing from your web browser will only print the information and citations listed on the web page

bull You may also display citations as plain text without the sidebar menu and toolbars by clicking the Text button

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Boolean Logic in PubMed

Boolean Logic is revealed by clicking Details

bull Entrez attempts to intelligently parse your queryQuery dna binding transcription factor macrophageDetails =gt ((((dna[MeSH Terms] OR dna[Text Word]) AND

((pharmacokinetics[MeSH Subheading] OR pharmacokineticsldquo [MeSH Terms]) OR binding [Text Word])) AND (transcription factorsldquo [MeSH Terms] OR transcription factor [Text Word])) AND (macrophages[MeSH Terms] OR macrophage [Text Word]))

bull You can force a Boolean searchQuery ldquodna bindingrdquo AND ldquotranscription factorrdquo AND

macrophageDetails =gt ((dna binding[All Fields] AND transcription

factor[All Fields]) AND (macrophages[MeSH Terms] OR macrophage[Text Word]))

Phrase Searching

bull Specify with quotesldquotranscription factorrdquo vs ldquotranscriptionrdquo

ldquofactorrdquo

bull Precomputedndash Fastndash Often mapped to synonyms and MeSH

termsndash Just because you get a ldquophrase not foundrdquo

message does not mean it is not present

Text Neighboring

Related articles link (single or multiple articles)ndash Term usage similarity

bull Articles talking about the same thing are likely to use the same words

ndash Good recall (sensitivity)ndash Precomputed and fast

Limitationsndash Strictly algorithmic no understanding

bull ldquoRas activates PI3Krdquo vs ldquoPI3K activates Rasrdquondash Historical and author biases in vocabularyndash Poor precision (specificity)ndash Ranking can not satisfy everyone

Computational Issues in Statistical Text Retrieval

bull Stop wordsndash Simple words like ldquotherdquo and ldquoandrdquo are not worth scoring

bull Term weightsndash We should weight matches of rare words more heavily than

matches of common wordsbull Stemming and synonyms

ndash Need to stem verbs and plural formsndash May or may not be able to reduce to a normalized set of

synonymsbull Normalizing for length

ndash Donrsquot want to exclude short articles or articles without an abstract

bull All vs all comparison is not feasiblendash 107 articles =gt 1014 comparisons not feasiblendash Compute demands of the task are growing faster than Moorersquos

law

Entrez Clipboard

bull The Clipboard gives you a place to collect selected citations from one search or several searches

bull After you add citations to the Clipboard you may then want to use the print save or order buttons

bull The maximum number of items that can be placed in the Clipboard is 500

bull Once you have added items to the Clipboard you can click on Clipboard from the Features bar to view your selections

bull PubMed Central uses cookies to add your selections to the Clipboard To use this feature your web browser must be set to accept cookies

Using Clipboard

bull Add to Clipboard ndash To place an item in the Clipboard click on the

check box to the left of the citationndash Select Clipboard from the Send to pull-down

menundash Then click the Send to button Once you have

added a citation to the Clipboard the record number color will change to green Send to ldquoclipboardrdquo

ndash You can save results collected from multiple searches

ndash The Clipboard will hold a maximum of 500 itemsndash Clipboard items will be lost after 1 hours of

inactivity

Saving from the Clipboard

bull Citations are initially displayed in the summary format in the relevancy order

bull Use Sort to change the order You can select all or individual citations to display or save in one of the citation display formats

bull Select the desired format from the pull-down menu click Save to save your selections to a file or use the Print feature of your web browser to print the citations

bull Printing from your web browser will only print the information and citations listed on the web page

bull You may also display citations as plain text without the sidebar menu and toolbars by clicking the Text button

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Boolean Logic is revealed by clicking Details

bull Entrez attempts to intelligently parse your queryQuery dna binding transcription factor macrophageDetails =gt ((((dna[MeSH Terms] OR dna[Text Word]) AND

((pharmacokinetics[MeSH Subheading] OR pharmacokineticsldquo [MeSH Terms]) OR binding [Text Word])) AND (transcription factorsldquo [MeSH Terms] OR transcription factor [Text Word])) AND (macrophages[MeSH Terms] OR macrophage [Text Word]))

bull You can force a Boolean searchQuery ldquodna bindingrdquo AND ldquotranscription factorrdquo AND

macrophageDetails =gt ((dna binding[All Fields] AND transcription

factor[All Fields]) AND (macrophages[MeSH Terms] OR macrophage[Text Word]))

Phrase Searching

bull Specify with quotesldquotranscription factorrdquo vs ldquotranscriptionrdquo

ldquofactorrdquo

bull Precomputedndash Fastndash Often mapped to synonyms and MeSH

termsndash Just because you get a ldquophrase not foundrdquo

message does not mean it is not present

Text Neighboring

Related articles link (single or multiple articles)ndash Term usage similarity

bull Articles talking about the same thing are likely to use the same words

ndash Good recall (sensitivity)ndash Precomputed and fast

Limitationsndash Strictly algorithmic no understanding

bull ldquoRas activates PI3Krdquo vs ldquoPI3K activates Rasrdquondash Historical and author biases in vocabularyndash Poor precision (specificity)ndash Ranking can not satisfy everyone

Computational Issues in Statistical Text Retrieval

bull Stop wordsndash Simple words like ldquotherdquo and ldquoandrdquo are not worth scoring

bull Term weightsndash We should weight matches of rare words more heavily than

matches of common wordsbull Stemming and synonyms

ndash Need to stem verbs and plural formsndash May or may not be able to reduce to a normalized set of

synonymsbull Normalizing for length

ndash Donrsquot want to exclude short articles or articles without an abstract

bull All vs all comparison is not feasiblendash 107 articles =gt 1014 comparisons not feasiblendash Compute demands of the task are growing faster than Moorersquos

law

Entrez Clipboard

bull The Clipboard gives you a place to collect selected citations from one search or several searches

bull After you add citations to the Clipboard you may then want to use the print save or order buttons

bull The maximum number of items that can be placed in the Clipboard is 500

bull Once you have added items to the Clipboard you can click on Clipboard from the Features bar to view your selections

bull PubMed Central uses cookies to add your selections to the Clipboard To use this feature your web browser must be set to accept cookies

Using Clipboard

bull Add to Clipboard ndash To place an item in the Clipboard click on the

check box to the left of the citationndash Select Clipboard from the Send to pull-down

menundash Then click the Send to button Once you have

added a citation to the Clipboard the record number color will change to green Send to ldquoclipboardrdquo

ndash You can save results collected from multiple searches

ndash The Clipboard will hold a maximum of 500 itemsndash Clipboard items will be lost after 1 hours of

inactivity

Saving from the Clipboard

bull Citations are initially displayed in the summary format in the relevancy order

bull Use Sort to change the order You can select all or individual citations to display or save in one of the citation display formats

bull Select the desired format from the pull-down menu click Save to save your selections to a file or use the Print feature of your web browser to print the citations

bull Printing from your web browser will only print the information and citations listed on the web page

bull You may also display citations as plain text without the sidebar menu and toolbars by clicking the Text button

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Phrase Searching

bull Specify with quotesldquotranscription factorrdquo vs ldquotranscriptionrdquo

ldquofactorrdquo

bull Precomputedndash Fastndash Often mapped to synonyms and MeSH

termsndash Just because you get a ldquophrase not foundrdquo

message does not mean it is not present

Text Neighboring

Related articles link (single or multiple articles)ndash Term usage similarity

bull Articles talking about the same thing are likely to use the same words

ndash Good recall (sensitivity)ndash Precomputed and fast

Limitationsndash Strictly algorithmic no understanding

bull ldquoRas activates PI3Krdquo vs ldquoPI3K activates Rasrdquondash Historical and author biases in vocabularyndash Poor precision (specificity)ndash Ranking can not satisfy everyone

Computational Issues in Statistical Text Retrieval

bull Stop wordsndash Simple words like ldquotherdquo and ldquoandrdquo are not worth scoring

bull Term weightsndash We should weight matches of rare words more heavily than

matches of common wordsbull Stemming and synonyms

ndash Need to stem verbs and plural formsndash May or may not be able to reduce to a normalized set of

synonymsbull Normalizing for length

ndash Donrsquot want to exclude short articles or articles without an abstract

bull All vs all comparison is not feasiblendash 107 articles =gt 1014 comparisons not feasiblendash Compute demands of the task are growing faster than Moorersquos

law

Entrez Clipboard

bull The Clipboard gives you a place to collect selected citations from one search or several searches

bull After you add citations to the Clipboard you may then want to use the print save or order buttons

bull The maximum number of items that can be placed in the Clipboard is 500

bull Once you have added items to the Clipboard you can click on Clipboard from the Features bar to view your selections

bull PubMed Central uses cookies to add your selections to the Clipboard To use this feature your web browser must be set to accept cookies

Using Clipboard

bull Add to Clipboard ndash To place an item in the Clipboard click on the

check box to the left of the citationndash Select Clipboard from the Send to pull-down

menundash Then click the Send to button Once you have

added a citation to the Clipboard the record number color will change to green Send to ldquoclipboardrdquo

ndash You can save results collected from multiple searches

ndash The Clipboard will hold a maximum of 500 itemsndash Clipboard items will be lost after 1 hours of

inactivity

Saving from the Clipboard

bull Citations are initially displayed in the summary format in the relevancy order

bull Use Sort to change the order You can select all or individual citations to display or save in one of the citation display formats

bull Select the desired format from the pull-down menu click Save to save your selections to a file or use the Print feature of your web browser to print the citations

bull Printing from your web browser will only print the information and citations listed on the web page

bull You may also display citations as plain text without the sidebar menu and toolbars by clicking the Text button

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Text Neighboring

Related articles link (single or multiple articles)ndash Term usage similarity

bull Articles talking about the same thing are likely to use the same words

ndash Good recall (sensitivity)ndash Precomputed and fast

Limitationsndash Strictly algorithmic no understanding

bull ldquoRas activates PI3Krdquo vs ldquoPI3K activates Rasrdquondash Historical and author biases in vocabularyndash Poor precision (specificity)ndash Ranking can not satisfy everyone

Computational Issues in Statistical Text Retrieval

bull Stop wordsndash Simple words like ldquotherdquo and ldquoandrdquo are not worth scoring

bull Term weightsndash We should weight matches of rare words more heavily than

matches of common wordsbull Stemming and synonyms

ndash Need to stem verbs and plural formsndash May or may not be able to reduce to a normalized set of

synonymsbull Normalizing for length

ndash Donrsquot want to exclude short articles or articles without an abstract

bull All vs all comparison is not feasiblendash 107 articles =gt 1014 comparisons not feasiblendash Compute demands of the task are growing faster than Moorersquos

law

Entrez Clipboard

bull The Clipboard gives you a place to collect selected citations from one search or several searches

bull After you add citations to the Clipboard you may then want to use the print save or order buttons

bull The maximum number of items that can be placed in the Clipboard is 500

bull Once you have added items to the Clipboard you can click on Clipboard from the Features bar to view your selections

bull PubMed Central uses cookies to add your selections to the Clipboard To use this feature your web browser must be set to accept cookies

Using Clipboard

bull Add to Clipboard ndash To place an item in the Clipboard click on the

check box to the left of the citationndash Select Clipboard from the Send to pull-down

menundash Then click the Send to button Once you have

added a citation to the Clipboard the record number color will change to green Send to ldquoclipboardrdquo

ndash You can save results collected from multiple searches

ndash The Clipboard will hold a maximum of 500 itemsndash Clipboard items will be lost after 1 hours of

inactivity

Saving from the Clipboard

bull Citations are initially displayed in the summary format in the relevancy order

bull Use Sort to change the order You can select all or individual citations to display or save in one of the citation display formats

bull Select the desired format from the pull-down menu click Save to save your selections to a file or use the Print feature of your web browser to print the citations

bull Printing from your web browser will only print the information and citations listed on the web page

bull You may also display citations as plain text without the sidebar menu and toolbars by clicking the Text button

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Computational Issues in Statistical Text Retrieval

bull Stop wordsndash Simple words like ldquotherdquo and ldquoandrdquo are not worth scoring

bull Term weightsndash We should weight matches of rare words more heavily than

matches of common wordsbull Stemming and synonyms

ndash Need to stem verbs and plural formsndash May or may not be able to reduce to a normalized set of

synonymsbull Normalizing for length

ndash Donrsquot want to exclude short articles or articles without an abstract

bull All vs all comparison is not feasiblendash 107 articles =gt 1014 comparisons not feasiblendash Compute demands of the task are growing faster than Moorersquos

law

Entrez Clipboard

bull The Clipboard gives you a place to collect selected citations from one search or several searches

bull After you add citations to the Clipboard you may then want to use the print save or order buttons

bull The maximum number of items that can be placed in the Clipboard is 500

bull Once you have added items to the Clipboard you can click on Clipboard from the Features bar to view your selections

bull PubMed Central uses cookies to add your selections to the Clipboard To use this feature your web browser must be set to accept cookies

Using Clipboard

bull Add to Clipboard ndash To place an item in the Clipboard click on the

check box to the left of the citationndash Select Clipboard from the Send to pull-down

menundash Then click the Send to button Once you have

added a citation to the Clipboard the record number color will change to green Send to ldquoclipboardrdquo

ndash You can save results collected from multiple searches

ndash The Clipboard will hold a maximum of 500 itemsndash Clipboard items will be lost after 1 hours of

inactivity

Saving from the Clipboard

bull Citations are initially displayed in the summary format in the relevancy order

bull Use Sort to change the order You can select all or individual citations to display or save in one of the citation display formats

bull Select the desired format from the pull-down menu click Save to save your selections to a file or use the Print feature of your web browser to print the citations

bull Printing from your web browser will only print the information and citations listed on the web page

bull You may also display citations as plain text without the sidebar menu and toolbars by clicking the Text button

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Entrez Clipboard

bull The Clipboard gives you a place to collect selected citations from one search or several searches

bull After you add citations to the Clipboard you may then want to use the print save or order buttons

bull The maximum number of items that can be placed in the Clipboard is 500

bull Once you have added items to the Clipboard you can click on Clipboard from the Features bar to view your selections

bull PubMed Central uses cookies to add your selections to the Clipboard To use this feature your web browser must be set to accept cookies

Using Clipboard

bull Add to Clipboard ndash To place an item in the Clipboard click on the

check box to the left of the citationndash Select Clipboard from the Send to pull-down

menundash Then click the Send to button Once you have

added a citation to the Clipboard the record number color will change to green Send to ldquoclipboardrdquo

ndash You can save results collected from multiple searches

ndash The Clipboard will hold a maximum of 500 itemsndash Clipboard items will be lost after 1 hours of

inactivity

Saving from the Clipboard

bull Citations are initially displayed in the summary format in the relevancy order

bull Use Sort to change the order You can select all or individual citations to display or save in one of the citation display formats

bull Select the desired format from the pull-down menu click Save to save your selections to a file or use the Print feature of your web browser to print the citations

bull Printing from your web browser will only print the information and citations listed on the web page

bull You may also display citations as plain text without the sidebar menu and toolbars by clicking the Text button

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Using Clipboard

bull Add to Clipboard ndash To place an item in the Clipboard click on the

check box to the left of the citationndash Select Clipboard from the Send to pull-down

menundash Then click the Send to button Once you have

added a citation to the Clipboard the record number color will change to green Send to ldquoclipboardrdquo

ndash You can save results collected from multiple searches

ndash The Clipboard will hold a maximum of 500 itemsndash Clipboard items will be lost after 1 hours of

inactivity

Saving from the Clipboard

bull Citations are initially displayed in the summary format in the relevancy order

bull Use Sort to change the order You can select all or individual citations to display or save in one of the citation display formats

bull Select the desired format from the pull-down menu click Save to save your selections to a file or use the Print feature of your web browser to print the citations

bull Printing from your web browser will only print the information and citations listed on the web page

bull You may also display citations as plain text without the sidebar menu and toolbars by clicking the Text button

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Saving from the Clipboard

bull Citations are initially displayed in the summary format in the relevancy order

bull Use Sort to change the order You can select all or individual citations to display or save in one of the citation display formats

bull Select the desired format from the pull-down menu click Save to save your selections to a file or use the Print feature of your web browser to print the citations

bull Printing from your web browser will only print the information and citations listed on the web page

bull You may also display citations as plain text without the sidebar menu and toolbars by clicking the Text button

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Document Display in PubMed

bull PubMed Central displays your search results in relevancy order by batches - the default is 20 citations per page

bull The Show pull-down menu allows you to change the number of citations displayed on a single page up to a maximum of 500 items To do this

bull From the Summary Page click on the Show pull-down menu and select a number To have all of the citations displayed on a single page select a number higher than the total number of your search results

bull Click the Display button to redisplay your citations according to your selection

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Modifying the Display

bull PubMed Central citations are initially displayed in a summary format You can choose to display other formats ndash Click on the Abstract Full Text PDF or

PubLink hyperlink for a specific citation ndash All Citations -Select a display format from

the Display pull-down menu and then click Display to view a different display or Links for all citations on the page

ndash Selected Citations - Click on the boxes to the left of each author to select specific citations and then select a format or Links from the Display pull-down menu and click Display

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Entrez History

bull Retrieve and use your search historyndash Boolean combinations of search results To

combine searches use before search number eg 2 AND 6

ndash Filtering of previous search resultsndash This can help you on big searches to

remember and build on your termsndash Search History will be lost after eight hours

of inactivity

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Address Fields

Find a local expert in PubMedldquoMarshall Universityrdquo AND (25755) [ad] OR ldquoWest

Virginiardquo [ad] NOT WVU [ad])

Need to think about all the ways people write addresses

ldquoJoan C Edwardsrdquo fails to pick up ldquoMUSOMrdquo Zip codes are very specific but only get about 70 since they might not list all authors zips

Wonrsquot catch co-authored articles with a remote collaborator

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Secondary Indexes

Find articles about a Genbank entry ndash Query ldquoL44140 [si]rdquo1 Robertson SP Twigg SR Sutherland-Smith AJ Biancalana V

Gorlin RJ Horn D Kenwrick SJ Kim CA Morava E Newbury-Ecob R Orstavik KH Quarrell OWSchwartz CE Shears DJ Suri M Kendrick-Jones J Wilkie AO OPD-spectrum Disorders Clinical Collaborative Group Localized mutations in the gene encoding the cytoskeletal protein filamin A cause diverse malformations in humans Nat Genet 2003 Apr33(4)487-91

2 Rivella S Palermo B Pelizon C Sala C Arrigo G Toniolo D Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression Genomics 1999 Nov 1562(1)11-20

3 Small K Iber J Warren ST Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats Nat Genet 1997 May16(1)96-9

4 Chen EY Zollo M Mazzarella R Ciccodicola A Chen CN Zuo L Heiner C Burough F Repetto M Schlessinger D DUrso M Long-range sequence analysis in Xq28 thirteen known and six candidate genes in 2194 kb of high GC DNA between the RCPGCP and G6PD loci Hum Mol Genet 1996 May5(5)659-68

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

PubMedCentral

bull US National Library of Medicines digital archive of life sciences journal literature

bull Full text of many journal archivesndash Not the most recent issuesndash Limited journal collection

bull Access to PMC is free and unrestrictedhttpwwwpubmedcentralnihgovaboutfaqhtml

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Related Articles

bull PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation as well as the MeSH headings assigned The best matches for each citation are pre-calculated and stored as a set

bull You may see a few citations without the Related Articles link These citations have not yet gone through the algorithm which takes several days

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Links

bull The Links pull-down menu provides access to the links between records in the Entrez databases All links except for Related Articles are included in the pull down menu

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

LinkOut

bull LinkOut provides links from PubMed and other Entrez databases to a wide variety of relevant web-accessible online resources including full-text publications

bull To see the full list of web-accessible online resources for an item select LinkOut from the Links pull-down menu

bull View the Abstract or Citation display formats to see if there is an icon link to full-text

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

PubMed Link

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

NCBI Bookshelf

bull The Bookshelf is a growing collection of biomedical books that can be searched directly

bull Accessible as in text annotations on many PubMed abstractsndash ldquoLinksrdquo =gt ldquoBooksrdquondash Automated phrase indices hyperlinked to

text books

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

OnlineBooks

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

Example of Books LinksJ Biol Chem 2003 Aug 28 [Epub ahead of print]

Phosphorylation of serine S337 of NF-kappa B p50 is critical for DNA binding

Hou S Guan H Ricciardi RP

Microbiology Biochemistry University of Pennsylvania Philadelphia PA 19342

It has been demonstrated that phosphorylation of the p50 subunit of NF-kappa B is required for efficient DNA binding yet the specific phospho-residues of p50 have not been determined In this study we substituted all of the serine and conserved threonine residues in the p50 Rel homology domain and identified three serine residues S65 S337 and S342 as critical for DNA binding without affecting dimerization While substitution with negatively charged aspartic acid at each of these positions failed to restore DNA binding substitution with threonine a potential phospho-acceptor retained DNA binding for residues 65 and 337 In particular S337 in a consensus site for PKA and other kinases was shown to be phosphorylated both in vitro and in vivo Importantly phosphorylation of S337 by PKA in vitro dramatically increased DNA binding of p50 This study shows for the first time that DNA binding ability of NF-kB p50 subunit is regulated through phosphorylation of residue S337 and has implications f o r both positive and negative control of NF-kappa B transcriptiont

PMID 12947093 [PubMed - as supplied by publisher]

NCBI Handbook

• PubMed
• PubMed Tutorial
• NCBI Entrez
• PubMed vs Google
• Entrez PubMed
• Relationships between the Entrez primary information resources
• Searching the Biomedical Literature
• PubMed Search results
• PubMed Entry
• Uses and Limits of MeSH
• MeSH Vocabulary
• Slide 12
• MeSH Homepage
• Structure of MeSH
• MeSH Full Listing
• Journals Database
• Boolean Logic
• Slide 18
• Boolean Logic in PubMed
• Slide 20
• Boolean Logic is revealed by clicking Details
• Phrase Searching
• Text Neighboring
• Computational Issues in Statistical Text Retrieval
• Entrez Clipboard
• Using Clipboard
• Saving from the Clipboard
• Document Display in PubMed
• Modifying the Display
• Entrez History
• Address Fields
• Secondary Indexes
• PubMedCentral
• Related Articles
• Links
• LinkOut
• PubMed Link
• NCBI Bookshelf
• OnlineBooks
• Example of Books Links
• NCBI Handbook