The purpose of computing is insight not The purpose of computing is insight not numbers.“numbers.“

R. W. Hamming (1962)R. W. Hamming (1962)

Angiogenesis: Culprits uncovereAngiogenesis: Culprits uncoveredd

The signaling pathway that leads frThe signaling pathway that leads from RAS to MYC culminates in the reom RAS to MYC culminates in the repression of the key anti-angiogenic fpression of the key anti-angiogenic f

actor, actor, thrombospondin-1.thrombospondin-1.

Cell, Vol. 104, 333–339, 2001

http://www.signaling-gateway.org/http://www.signaling-gateway.org/

Watnick, R. S. Watnick, R. S. et alet al. Ras modulates Myc a. Ras modulates Myc activity to repress thrombospondin-1 expresctivity to repress thrombospondin-1 expression and increase tumor angiogenesis. sion and increase tumor angiogenesis. CaCancer Cellncer Cell 33, 219–231 (2003), 219–231 (2003)

6093

7057

Transcription ControlTranscription Control

to minimize false positivesto minimize false positives

to minimize false negativesto minimize false negatives

Protein-Protein Protein-Protein InteractionInteraction

The change of the meaning of The change of the meaning of protein functionprotein function

Protein-Protein Protein-Protein Interaction:Interaction:

Physical InteractionPhysical Interaction

Gene OntologyGene Ontology

Biological ProcessBiological Process

Molecular FunctionMolecular Function

Cellular LocalizationCellular Localization

Nature Genetics Vol 25, p25Nature Genetics Vol 25, p25

Nature Biotech 18: p1257Nature Biotech 18: p1257

Nature Biotech 18: p1257Nature Biotech 18: p1257

PNAS 2001 vol. 98 4277–4278

Protein-Protein Protein-Protein Interaction:Interaction:

Function AssociationFunction Association

The Rosetta Stone method for The Rosetta Stone method for detecting functional linkagedetecting functional linkage

NATURE VOL 405 , p823, 2000

Phylogenetic ProfilingCurrent Opinion in Chemical Biology 2001, 5:46–50

Gene OrderGene Order

Protein-Protein InteractiProtein-Protein Interactionon

InterologsInterologs

InterologsInterologsSCIENCE VOL 287 p116SCIENCE VOL 287 p116

SCIENCE VOL 295 p127

DatabaseDatabase

DIPDIP

BINDBIND

GRIDGRID

DIPDIP

http://dip.doe-mbi.ucla.edu/http://dip.doe-mbi.ucla.edu/

ROCK1 (LocusLink: 6093)ROCK1 (LocusLink: 6093)

4869N

BLASTPBLASTP

NP_593165

BINDBIND

http://www.bind.ca/http://www.bind.ca/

http://www.bind.ca/http://www.bind.ca/

GRIDGRID

http://biodata.mshri.on.ca/grid/http://biodata.mshri.on.ca/grid/

http://biodata.mshri.on.ca/grid/http://biodata.mshri.on.ca/grid/

IPPREDIPPRED

http://cbi.labri.fr/outils/ippred/IS_part_simple.phphttp://cbi.labri.fr/outils/ippred/IS_part_simple.php

Two seq

PredictomePredictome

...... is a tool for visualizing the predicted fun is a tool for visualizing the predicted functional associations among genes and protctional associations among genes and proteins in many different organisms. Associatieins in many different organisms. Associations, or gene links, are created using a varions, or gene links, are created using a variety of techniques, both experimental (yeasety of techniques, both experimental (yeast two-hybrid, immuno-coprecipitation, corret two-hybrid, immuno-coprecipitation, correlated expression) and computational (gene lated expression) and computational (gene fusion, chromosomal proximity, gene co-efusion, chromosomal proximity, gene co-evolution). volution).

...... is based on the premise that genes, or is based on the premise that genes, or their protein products, can be linked using their protein products, can be linked using both experimental and computational both experimental and computational techniques. Functional information about techniques. Functional information about individual proteins is then assessed in a individual proteins is then assessed in a network context, where characteristics network context, where characteristics about a protein can be inferred using the about a protein can be inferred using the functional traits of neighbors, the functional traits of neighbors, the neighbors of neighbors, etc. neighbors of neighbors, etc.

...... is intended as a central repository of the is intended as a central repository of the predicted links between proteins. The predicted links between proteins. The interface also includes modules that interface also includes modules that facilitate browsing and interpreting these facilitate browsing and interpreting these links. links.

http://genome-www.stanford.edu/Shttp://genome-www.stanford.edu/Saccharomyces/accharomyces/

http://predictome.bu.edu/http://predictome.bu.edu/

PathBlast: pathway alignment PathBlast: pathway alignment http://www.pathblast.org/bioc/pathblast/blastpathway.jsphttp://www.pathblast.org/bioc/pathblast/blastpathway.jsp