Software

Human and Animals

Homo sapiens	Mus musculus	Danio rerio	Drosophila melanogaster	Caenorhabditis elegans

Plants

Arabidopsis thaliana	Oryza sativa	Glycine max

Fungi

Saccharomyces cerevisiae	Cryptococcus neoformans

Bacteria

Pseudomonas aeruginosa	Escherichia coli

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

COEXPEDIA is currently available for human and mouse.

TRRUST: A reference database of human TF-target interactions

TRRUST (Transcriptional Regulatory relationships Unraveled by Sentence-based Text mining) is currently available for only human genes.

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

MUFFINN (MUtations For Functional Impact on Network Neighbors).

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

Morphin (Model Organisms Projected on a Human Integrated Gene Network) is currently available.

JiffyNet:Instant gene network building server for newly sequenced species

Jiffy (instant) gene network modeler for newly sequenced species

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

RIDDLE (Reflective diffusion and local extension) is currently available for only human genes.

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

Project Page