Difference between revisions of "Software"
From Bioinformatics Lab
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| − | ==''' | + | =='''Gene Regulation Research Tools'''== |
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': A reference database of TF-target interactions in human and mouse | [[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': A reference database of TF-target interactions in human and mouse | ||
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=='''Network Medicine Tools '''== | =='''Network Medicine Tools '''== | ||
| − | [[File: | + | [[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data |
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| + | [[File:Coexpedia.png |150px|link=http://www.coexpedia.org]] '''COEXPEDIA''': Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH) | ||
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[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only) | [[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only) | ||
| − | =='''Co-functional | + | |
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| + | =='''Co-functional Gene Networks'''== | ||
==''Human and Laboratory Animals''== | ==''Human and Laboratory Animals''== | ||
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==''Bacteria''== | ==''Bacteria''== | ||
{|border="0" width="200" | {|border="0" width="200" | ||
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|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]] | |align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]] | ||
| + | |align="center"|[[File:Staphnet_logo.JPG|150px|link=http://www.inetbio.org/staphnet]] | ||
| + | |align="center"|[[File:KlebNet_logo.png|150px|link=http://www.inetbio.org/klebnet]] | ||
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]] | |align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]] | ||
|align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]] | |align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]] | ||
|- | |- | ||
| − | |align="center"|Methicillin-resistant ''Staphylococcus aureus'' | + | |align="center"|''Pseudomonas aeruginosa (human pathogen)'' |
| − | |align="center"|'' | + | |align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)'' |
| − | |align="center"|''Escherichia coli'' | + | |align="center"|''Klebsiella pneumoniae (human pathogen)'' |
| − | |align="center"|''Xanthomonas oryzae pv. oryzae'' | + | |align="center"|''Escherichia coli (popular lab/factory bacterial species)'' |
| + | |align="center"|''Xanthomonas oryzae pv. oryzae (rice pathogen)'' | ||
|} | |} | ||
Revision as of 17:11, 21 December 2017
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 bacterial species) | 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)
