Software

Gene Regulation Research Tools

TRRUST: A reference database of TF-target interactions in human and mouse

Network Medicine Tools

COEXPEDIA: Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)

GWAB: A web server for network-based boosting of human genome-wide association data

MUFFINN: Cancer gene discovery via network analysis of somatic mutation data

MORPHIN: Network-assisted prediction of disease pathways in model organisms

RIDDLE: Network-assisted Gene Set Analysis (human only)

Human and Laboratory Animals

Homo sapiens	Mus musculus	Danio rerio	Drosophila melanogaster	Caenorhabditis elegans

Plants

Arabidopsis thaliana	Zea mays	Oryza sativa	Triticum aestivum	Glycine max	Solanum lycopersicum

Fungi

Saccharomyces cerevisiae	Cryptococcus neoformans

Bacteria

Methicillin-resistant Staphylococcus aureus	Pseudomonas aeruginosa	Escherichia coli	Xanthomonas oryzae pv. oryzae

Build your own co-functional networks

JiffyNet: Instant gene network building server for newly sequenced species

Domain-based PPI networks by Weighted Mutual Information (WMI)

Project Page

Domain2Pathway by Pathway Specificity (PS)

Project Page