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Microbiome Research

Hrgm logo.png HRGM: A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins

Mrgm logo.png MRGM: A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins

Single-cell Biology

ScHumanNet github scHumanNet: Cell-type-specific functional gene networks using single-cell RNA-sequencing data

VC logo.png VirtualCytometry: A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.

Network Medicine

HumanNet logo with title.pngHumanNet: Human gene networks for disease research

TRRUST logo.jpg TRRUST: Curated TF-target interaction networks in human and mouse

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

Ngsea logo1.png NGSEA: Network-augmented gene set enrichment analysis tool

Cover title muffinn.png MUFFINN: Cancer gene discovery via network analysis of somatic mutation data

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

Logo morphin.png MORPHIN: Network-assisted prediction of disease pathways in model organisms

Cover title riddle.jpg RIDDLE: Network-assisted Gene Set Analysis (human only)

Functional Gene Networks


MouseNetLogo.png Danionet logo.png Flynet.png WormNetv3.jpg
Mus musculus Danio rerio Drosophila melanogaster Caenorhabditis elegans


Aranet v2.jpg Maizenet logo 4th.png RiceNetv2 logo.png WheatNet logo.png BarleyNet logo.png Soynetlogo.png Tomatonet logo.png
Arabidopsis thaliana Zea mays Oryza sativa Triticum aestivum Hordeum vulgare Glycine max Solanum lycopersicum


Tools YesatNetLogo.jpg CryptoNet.png
Saccharomyces cerevisiae Cryptococcus neoformans


Pseudomonas logo.jpg Staphnet logo.JPG KlebNet logo.png EcoliNet.png XooNet logo.png
Pseudomonas aeruginosa (human pathogen) Methicillin-resistant Staphylococcus aureus (human pathogen) Klebsiella pneumoniae (human pathogen) Escherichia coli (popular lab/factory bacterial species) Xanthomonas oryzae pv. oryzae (rice pathogen)

Build your own Functional gene networks

BiomeNet logo.png BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome

Network-augmented GWAS Analysis for Arabidopsis

AraGWAB logo.png araGWAB: genome-wide association boosting for Arabidopsis thaliana

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

Project Page

Domain2Pathway by Pathway Specificity (PS)

Project Page

Personal tools