Large-scale data and text mining

Large-scale data and text mining

Lars Juhl Jensen

function prediction

Jensen, Gupta et al., Journal of Molecular Biology, 2002

cell-cycle regulation

de Lichtenberg, Jensen et al., Science, 2005

Jensen, Jensen, de Lichtenberg et al., Nature, 2006

phosphorylation

signaling networks

upstream events

downstream events

NetworKIN

sequence motifs

NetPhorest

automated pipeline

Miller, Jensen et al., Science Signaling, 2008

data organization

Miller, Jensen et al., Science Signaling, 2008

compilation of datasets

redundancy reduction

training and evaluation

motif atlas

model organisms

other modifications

protein networks

functional associations

STRING

Jensen, Kuhn et al., Nucleic Acids Research, 2009

630 genomes

genomic context

Korbel et al., Nature Biotechnology, 2004

Korbel et al., Nature Biotechnology, 2004

Korbel et al., Nature Biotechnology, 2004

physical interactions

Jensen & Bork, Science, 2008

genetic interactions

Beyer et al., Nature Reviews Genetics, 2007

gene coexpression

curated knowledge

Letunic & Bork, Trends in Biochemical Sciences, 2008

literature mining

>10 km

confidence scores

cross-species integration

visualization

Frishman et al., Modern Genome Annotation, 2009

small molecules

STITCH

Kuhn et al., Nucleic Acids Research, 2008

kinase inhibitor screens

Fedorov et al., PNAS, 2007

new targets for old drugs

chemical similarity

Campillos & Kuhn et al., Science, 2008

side-effect similarity

information on side effects

package inserts

Campillos, Kuhn et al., Science, 2008

text mining

side-effect ontology

Campillos, Kuhn et al., Science, 2008

side-effect correlations

Campillos, Kuhn et al., Science, 2008

side-effect frequencies

Campillos & Kuhn et al., Science, 2008

combined similarity score

Campillos, Kuhn et al., Science, 2008

thousands of predictions

categorization

Campillos, Kuhn et al., Science, 2008

20 drug–drug relations

Campillos, Kuhn et al., Science, 2008

in vitro binding assays

Ki<10 µM for 11 of 20

cell assays

9 of 9 showed activity

augmented browsing

Reflect

collaborate publishers

AcknowledgmentsNetPhorest.info

– Rune Linding– Martin Lee Miller– 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

STRING-DB.org– Christian von Mering– 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

STITCH-DB.org– Michael Kuhn– Damian Szklarczyk– Andrea Franceschini– Monica Campillos– Christian von Mering– Lars Juhl Jensen– Andreas Beyer– Peer Bork

NetworKIN.info– Rune Linding– Gerard Ostheimer– Heiko Horn– 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

– Reflect.ws– Sean O’Donoghue– Heiko Horn– Evangelos Pafilis– Michael Kuhn– Nigel Brown– Reinhardt Schneider

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