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 | ||
− | ==''Human and Animals''== | + | |
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+ | =='''Network Medicine Tools '''== | ||
+ | [[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:GWAB_logo.png |150px|link=http://www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association 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:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms | ||
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+ | [[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only) | ||
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+ | =='''Co-functional Gene Networks'''== | ||
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+ | ==''Human and Laboratory Animals''== | ||
+ | {|border="0" width="500" | ||
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]] | |align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]] | ||
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]] | |align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]] | ||
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==''Plants''== | ==''Plants''== | ||
− | {|border="0" width=" | + | {|border="0" width="400" |
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]] | |align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]] | ||
+ | |align="center"|[[File:Maizenet_logo_4th.png|150px|link=http://www.inetbio.org/maizenet]] | ||
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]] | |align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]] | ||
+ | |align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]] | ||
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]] | |align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]] | ||
+ | |align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]] | ||
|- | |- | ||
|align="center"|''Arabidopsis thaliana'' | |align="center"|''Arabidopsis thaliana'' | ||
+ | |align="center"|''Zea mays'' | ||
|align="center"|''Oryza sativa'' | |align="center"|''Oryza sativa'' | ||
+ | |align="center"|''Triticum aestivum'' | ||
|align="center"|''Glycine max'' | |align="center"|''Glycine max'' | ||
+ | |align="center"|''Solanum lycopersicum'' | ||
|} | |} | ||
==''Fungi''== | ==''Fungi''== | ||
− | {|border="0" width=" | + | {|border="0" width="200" |
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]] | |align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]] | ||
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]] | |align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]] | ||
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==''Bacteria''== | ==''Bacteria''== | ||
− | {|border="0" width=" | + | {|border="0" width="200" |
|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]] | ||
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− | |align="center"|''Pseudomonas aeruginosa'' | + | |align="center"|''Pseudomonas aeruginosa (human pathogen)'' |
− | |align="center"|''Escherichia coli'' | + | |align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)'' |
+ | |align="center"|''Klebsiella pneumoniae (human pathogen)'' | ||
+ | |align="center"|''Escherichia coli (popular lab/factory bacterial species)'' | ||
+ | |align="center"|''Xanthomonas oryzae pv. oryzae (rice pathogen)'' | ||
|} | |} | ||
+ | ==''Build your own co-functional networks''== | ||
+ | [[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]] | ||
+ | '''JiffyNet''': Instant gene network building server for newly sequenced species | ||
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+ | =='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''== | ||
+ | [[WMI|<big>'''Project Page'''</big>]] | ||
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− | + | =='''Domain2Pathway by Pathway Specificity (PS) '''== | |
− | + | [[PS|<big>'''Project Page'''</big>]] | |
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− | ==''' | + | |
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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
Homo sapiens | Mus musculus | Danio rerio | Drosophila melanogaster | Caenorhabditis elegans |
Plants
Arabidopsis thaliana | Zea mays | Oryza sativa | Triticum aestivum | Glycine max | Solanum lycopersicum |
Fungi
Saccharomyces cerevisiae | Cryptococcus neoformans |
Bacteria
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)