Making gene networks through data integration

Lars Juhl Jensen

association networks

guilt by association

molecular networks

proteins

string-db.org

small molecules

stitch-db.org

non-coding RNAs

compartments

compartments.jensenlab.org

tissues

tissues.jensenlab.org

diseases

data integration

computational predictions

gene neighborhood

Korbel et al., Nature Biotechnology, 2004

TargetScan

experimental data

gene expression

protein interactions

Jensen & Bork, Science, 2008

miRTarBase

curated knowledge

metabolic pathways

Letunic & Bork, Trends in Biochemical Sciences, 2008

signaling pathways

many databases

different formats

different identifiers

variable quality

not comparable

hard work

(Ph.D. students)

common identifiers

quality scores

von Mering et al., Nucleic Acids Research, 2005

score calibration

von Mering et al., Nucleic Acids Research, 2005

homology-based transfer

Franceschini et al., Nucleic Acids Research, 2013

missing most of the data

text mining

>10 km

too much to read

computer

as smart as a dog

teach it specific tricks

named entity recognition

comprehensive lexicon

let-7a-3p

let-7a*

flexible matching

let-7a

let7a

name expansions

let-7a

miR-let-7a

“black list”

SDS

co-mentioning

counting

within documents

within paragraphs

within sentences

high recall

high precision

fuzzy associations

NLPNatural Language Processing

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]

extract stated facts

high precision

poor recall

Jensen et al., Nature Reviews Genetics, 2006

questions?