Difference between revisions of "Software"

Revision as of 16:04, 22 October 2016

Co-functional networks: Organism-specific network-assisted hypothesis generation servers

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

Other Network Biology tools

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

TRRUST (Transcriptional Regulatory relationships Unraveled by Sentence-based Text mining): A reference database of human TF-target interactions

MUFFINN (MUtations For Functional Impact on Network Neighbors): cancer gene discovery via network analysis of somatic mutation data

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