Advanced bioinformaticsmethods for proteomics

Lars Juhl Jensen

three parts

signaling networks

association networks

text mining

Part 1signaling networks

phosphoproteomics

Linding, Jensen, Ostheimer et al., Cell, 2007

in vivo phosphosites

kinases are unknown

sequence specificity

Miller, Jensen et al., Science Signaling, 2008

NetPhorest

Miller, Jensen et al., Science Signaling, 2008

motif atlas

kinases

phospho-binding proteins

phosphatases

protein-specific

no context

co-activators

protein scaffolds

localization

expression

association network

Linding, Jensen, Ostheimer et al., Cell, 2007

NetworKIN

Linding, Jensen, Ostheimer et al., Cell, 2007

web interface

Part 2association networks

guilt by association

STRING

Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011

>1100 genomes

computational predictions

genomic context

gene fusion

Korbel et al., Nature Biotechnology, 2004

phylogenetic profiles

Korbel et al., Nature Biotechnology, 2004

experimental data

physical interactions

Jensen & Bork, Science, 2008

gene coexpression

curated knowledge

pathways

Letunic & Bork, Trends in Biochemical Sciences, 2008

many databases

different formats

different identifiers

variable quality

not comparable

quality scores

von Mering et al., Nucleic Acids Research, 2005

calibrate vs. gold standard

von Mering et al., Nucleic Acids Research, 2005

missing most of the data

Part 3text mining

>10 km

too much to read

computer

as smart as a dog

teach it specific tricks

named entity recognition

comprehensive lexicon

proteins

cellular components

compartments.jensenlab.org

tissues

tissues.jensenlab.org

diseases

orthographic variation

singular vs. plural

spaces and hyphens

“black list”

information extraction

co-mentioning

NLPNatural Language Processing

Gene and protein names

Cue words for entity recognition

Verbs for relation extraction

[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]

summary

bioinformatics

more than BLAST

data/text mining

save you much time

AcknowledgmentsNetPhorestRune Linding

Martin Lee Miller

Erwin Schoof

Francesca Diella

Claus Jørgensen

Michele Tinti

Lei Li

Marilyn Hsiung

Sirlester A. Parker

Jennifer Bordeaux

Thomas Sicheritz-Pontén

Marina Olhovsky

Adrian Pasculescu

Jes Alexander

Stefan Knapp

Nikolaj Blom

Peer Bork

Shawn Li

Gianni Cesareni

Tony Pawson

Benjamin E. Turk

Michael B. Yaffe

Søren Brunak

STRINGChristian von Mering

Damian Szklarczyk

Michael Kuhn

Manuel Stark

Samuel Chaffron

Chris Creevey

Jean Muller

Tobias Doerks

Philippe Julien

Alexander Roth

Milan Simonovic

Jan Korbel

Berend Snel

Martijn Huynen

Peer Bork

NetworKINRune Linding

Heiko Horn

Gerard Ostheimer

Martin Lee Miller

Francesca Diella

Karen Colwill

Jing Jin

Pavel Metalnikov

Vivian Nguyen

Adrian Pasculescu

Jin Gyoon Park

Leona D. Samson

Rob Russell

Peer Bork

Michael Yaffe

Tony Pawson

Text-miningSune Frankild

Evangelos Pafilis

Janos Binder

Heiko Horn

Michael Kuhn

Nigel Brown

Reinhardt Schneider

Sean O’Donoghue

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