Advanced bioinformaticsof proteomics datasets

Lars Juhl Jensen

three parts

signaling networks

association networks

text mining

signaling networks

MS-based proteomics

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

in vivo PTM sites

actors are unknown

sequence specificity

logo plots

Miller, Jensen et al., Science Signaling, 2008

motif collections

Eukaryotic Linear Motifs

regular expressions

[VILMAFP](K).E

NetPhorest

machine learning

kinases

phospho-binding proteins

phosphatases

Miller, Jensen et al., Science Signaling, 2008

possible actors

no cellular 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

association networks

guilt by association

STRING

2000+ genomes

computational predictions

gene fusion

Korbel et al., Nature Biotechnology, 2004

gene neighborhood

Korbel et al., Nature Biotechnology, 2004

phylogenetic profiles

Korbel et al., Nature Biotechnology, 2004

experimental data

gene coexpression

protein interactions

Jensen & Bork, Science, 2008

curated knowledge

pathways

Letunic & Bork, Trends in Biochemical Sciences, 2008

many databases

different formats

different identifiers

variable quality

not comparable

not same species

hard work

(Ph.D. students)

parsers

common identifiers

clever ideas

quality assessment

scoring schemes

affinity purification

von Mering et al., Nucleic Acids Research, 2005

score calibration

gold standard

von Mering et al., Nucleic Acids Research, 2005

implicit weighting by quality

common scale

interologs

homology-based transfer

orthologous groups

Franceschini et al., Nucleic Acids Research, 2013

missing most of the data

text mining

>10 km

too much to read

exponential growth

~40 seconds per paper

computer

as smart as a dog

teach it specific tricks

named entity recognition

comprehensive lexicon

CDC2

cyclin dependent kinase 1

orthographic variation

expansion rules

prefixes and suffixes

CDC2

hCdc2

flexible matching

spaces and hyphens

cyclin dependent kinase 1

cyclin-dependent kinase 1

“black list”

SDS

information extraction

co-mentioning

counting

within documents

within paragraphs

within sentences

scoring scheme

score calibration

natural language processing

grammatical analysis

what you learned in schoolpronoun pronoun verb preposition noun

Gene and protein namesCue words for entity

recognitionVerbs for relation extraction

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

complex sentences

summary

computational approaches

data integration

text mining

scoring schemes

general approach

protein networks

string-db.org

chemical networks

stitch-db.org

subcellular localization

compartments.jensenlab.org

tissue expression

tissues.jensenlab.org

disease associations