© 2004 by genomatix software gmbh genomatix dr. martin seifert genomatix software gmbh landsberger...
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© 2004 by Genomatix Software GmbH
Genomatix
Dr. Martin Seifert
Genomatix Software GmbH
Landsberger Strasse 6, D-80339 München
http://www.genomatix.de
© 2004 by Genomatix Software GmbH
Genomatix
What data/analysis tools does Genomatix offer?
What does Genomatix mean by “understanding gene regulation” ?
How to apply the data & tools to “understand gene regulation” ?
Which data/analysis tools will support my work best?
© 2004 by Genomatix Software GmbH
Genomatix
Overview
Introduction to gene expression
Regulation of gene expression
Gene regulation in a genomic view
© 2004 by Genomatix Software GmbH
Genomatix
the correct genes…
…are expressed inthe correct cell…
…at correct levels.
Introduction to gene expression
…over correct time intervalls…
Prerequisite for correct cell behaviour
© 2004 by Genomatix Software GmbH
Genomatix
the correct genes…
…are expressed inthe correct cell…
…at correct levels.…over correct time intervalls…
What if…
“additional gene”
“gene loss”
“overexpression”“wrong time intervall”
Introduction to gene expression
© 2004 by Genomatix Software GmbH
Genomatix
Summary
Correct cell behavior requires expression of…
correct set of genes
in time
at the correct level
tough logistic task !
Introduction to gene expression
© 2004 by Genomatix Software GmbH
Genomatix
Overview
Introduction to gene expression
Regulation of gene expression
Gene regulation in a genomic view
© 2004 by Genomatix Software GmbH
Genomatix
Coding exons
First exon
Schematic organization of a gene - GLOSSARY
Promoter
DNA
Non-coding exon
Regulation of gene expression
© 2004 by Genomatix Software GmbH
Genomatix
Chromatin activation
Translation
Gene expression steps
Epigenetics
Protein
Processed protein
G-ppp-
Primary transcript
G-ppp-
Primary transcript
Genomic sequence
Transcription
Mature mRNA
Regulation of gene expression
© 2004 by Genomatix Software GmbH
Genomatix
Gene regulation – Transcription regulation
Protein complex
binding
Regulatory network
Regulation of gene expression
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Example: Diabetes (MODY)
Protein complex
binding
Regulatory network
Regulation of gene expression
Insulin
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Key – lock principle
TFIIB TFIIE
TFIIH
INR
TFIID TFIIF
RNA polymerase II
TFIIA
TBP
proximal promoter
core promoter
distal promoter/enhancer
TF binding sites
„DNA-looping“
TATA
TF binding sites
Transcription factor binding sites
Protein complex
binding
Regulation of gene expression
© 2004 by Genomatix Software GmbH
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Dependencies in expression regulation
Promoter of Gene A
Gene YGene X Gene Z Gene T
Regulation of gene expression
Protein
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One lock – different keys
TFIIB TFIIE
TFIIH TFIID TFIIF TFIIA
TBP TATA
TFIIB TFIIE
TFIIH
INR
TFIID TFIIF TFIIA
TBP TATA
Same lock – different keys: Same gene - different biological context
Regulation of gene expression
© 2004 by Genomatix Software GmbH
Genomatix
Promoter logic
Which combination is functional ?
50 TFBs =
One promoter – many transcription factor binding sites (TFBs)
Need help ?
Regulation of gene expression
1.125.899.906.842.624 combinations
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Genomatix
Example: Analysis of the RANTES promoter
Fessele, S., Maier, H., Zischek, C., Nelson, P.J., Werner, T. (2002) Regulatory context is a crucial part of gene functionTrends in Genetics 18, 60-63 (MEDLINE 1181130)
Regulation of gene expression
© 2004 by Genomatix Software GmbH
Genomatix
Summary
Understanding gene regulation : understanding transcription regulation
The promoter of a gene is the element to “unlock” gene expression
The key to “unlock” gene expression is a protein complex
Different keys can unlock the same promoter
Promoter analysis: Find all keys (protein complexes) which can unlock.
Protein complex requires expression of genes -> gene dependencies
© 2004 by Genomatix Software GmbH
Genomatix
Overview
Introduction to gene expression
Regulation of gene expression
Gene regulation in a genomic view
© 2004 by Genomatix Software GmbH
Genomatix
One gene = one promoter ?
Genes can have alternative transcripts with alternative promoters
Gen A
Gen A
Gen A
Gene regulation in a genomic view
© 2004 by Genomatix Software GmbH
Genomatix
Comparative genomic map of the Glucokinase GCK
Promoterset 1 Promoterset 2
Hepatic promoter
Pancreatic promoter
Tanisawa et al., Mol. Endocrinol. 6, 1070-1081, 1992.
Data from ElDorado
Gene regulation in a genomic view
© 2004 by Genomatix Software GmbH
Genomatix
TF- genes with one
promoter. 51%
Mammalian TFs genes are enriched in alternative promoters
TF- genes with Alternative transcripts
and alternative promoters. 49%
All genes Transcription factors
Genes with alternative transcripts and one promoter. 17%
Genes with Alternative transcripts
and alternative promoters. 28%
Genes with one transcript. 55%
Data from ElDorado
Gene regulation in a genomic view
© 2004 by Genomatix Software GmbH
Genomatix
transcript resolvingexpression array
Pathway oriented expression analysis on microarrays
Knowledge of alternative promoters enables transcript-specific probe design
conventional Expression array
3’-probetranscript-specific probes
Gene regulation in a genomic view
© 2004 by Genomatix Software GmbH
Genomatix
Alternative mapping of probes to genes for Affymetrix chipsLaurent Gautier*1 , Morten Møller 2 , Lennart Friis-Hansen 2 and
Steen Knudsen 1
Results: In a large number of cases, 36%, the probes matching a reference sequence were consistent with the grouping of probes by the manufacturer of the chips. For the remaining cases there were discrepancies and we show how that can affect the analysis of data.
Conclusions: While the probes on Affymetrix arrays remain the same for several years,the biological knowledge concerning the genomic sequences evolves rapidly. Using up-to-date knowledge can apparently change the outcome of an analysis.
Methods: We investigated how probes found on recent commercial microarrays for human genes (Affymetrix HG-U133A) were matching a recent curated collection of human transcripts:the NCBI RefSeq database
BMC Bioinformatics. 2004 Aug 14;5(1):111
Genome annotation
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Summary
A gene can have alternative promoters and alternative transcripts
For gene regulation oriented microarray analysis genome annotation is important
Alternative promoter usage can be tissue and context specific
© 2004 by Genomatix Software GmbH
Genomatix
BiblioSphere
Literature data mining strategy using more than 350.000 quality Checked gene names, synonyms & Genomatix proprietary semantic relation concepts
3-D interactive view of gene relationships
Context sensitive disambiguation techniques to minimize the number of false positive matches.
Search strategy allows not only to find direct gene-gene co-citations but also yet unknown gene relations via interlinks.
BiblioSphere
© 2004 by Genomatix Software GmbH
Genomatix
BiblioSphere
Classification of results with biological meaningful filters: Tissue, Gene Ontology and MeSH
Statistical rating by z-scores for Gene Ontology, MeSH and tissue filters indicating over and under representation of co-cited genes in the referring biological categories
Transcription factor analysis of the promoters of co-cited genes
Literature analysis and evaluation by additional lines of evidences!
Full interconnection with GEMSLauncher and ElDorado
BiblioSphere
© 2004 by Genomatix Software GmbH
Genomatix
ElDorado genome annotation and analysis
Most comprehensive genome annotation for regulatory regions andtranscripts
Integrated promoter annotation by promoter modules, pre-calculated byGEMS Launcher
ElDorado
Comparative genomics to detect and annotate unknown promoter regions (patent pending)
Integrated SNP annotation according to effects for gene regulationand protein level
Full interconnection with GEMSLauncher and BiblioSphere
© 2004 by Genomatix Software GmbH
Genomatix GEMSLauncher
Genomic sequences, mRNA, cDNA, SNPs
SMARTest Exon Mapper
Promoters
PromterInspectorSequenceAnnotation
S/MAR Exon/Intron structure
Experimental results and literature
TF Binding sites Modules, LTR,
Genomic repeatMatDefine
SMAR
Librarys
MatInspector
SequenceShaperSNPInspector ModellInspector
FastMFrameWorker
ModelsAnalysis
Modelling
© 2004 by Genomatix Software GmbH
Genomatix Genomatix
Genomic sequences, mRNA, cDNA, SNPs
Bridging the gap between sequences, literature and experimental results
Experimenteal results
Genome annotation
Literature mining Sequence analysis
ElDorado
BiblioSphere GEMS Launcher
Understandinggene regulation
Literature