Software
Gene Regulation Research Tools
TRRUST: A reference database of TF-target interactions in human and mouse
Network Medicine Tools
MUFFINN: Cancer gene discovery via network analysis of somatic mutation data
GWAB: A web server for network-based boosting of human genome-wide association data
COEXPEDIA: Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)
MORPHIN: Network-assisted prediction of disease pathways in model organisms
RIDDLE: Network-assisted Gene Set Analysis (human only)
Co-functional Gene Networks
Human and Laboratory Animals
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| Homo sapiens | Mus musculus | Danio rerio | Drosophila melanogaster | Caenorhabditis elegans |
Plants
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| Arabidopsis thaliana | Zea mays | Oryza sativa | Triticum aestivum | Glycine max | Solanum lycopersicum |
Fungi
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| Saccharomyces cerevisiae | Cryptococcus neoformans |
Bacteria
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| Pseudomonas aeruginosa (human pathogen) | Methicillin-resistant Staphylococcus aureus (human pathogen) | Klebsiella pneumoniae (human pathogen) | Escherichia coli (popular lab/factory bacterium) | Xanthomonas oryzae pv. oryzae (rice pathogen) |
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)
