Wednesday, June 1, 2011

Resources for Pathway Analysis, Functional Annotation, and Interactome Reconstruction with Omics Data

I just read a helpful paper on pathway analysis and interactome reconstruction:

Tieri, P., Fuente, A. D., Termanini, A., & Franceschi, C. (2011). Integrating Omics Data for Signaling Pathways, Interactome Reconstruction, and Functional Analysis. In Bioinformatics for Omics Data, Methods in Molecular Biology, vol. 719. doi: 10.1007/978-1-61779-027-0. (PubMed).

The authors give a description about how each of these tools can be used in pathway analysis and functional annotation, along with an example of using several of these resources for mapping the interactome for transcription factor NF-kappa-B.

While a more extensive list of hundreds of tools and databases for biological pathway analysis can be found at Pathguide, this looks like a good starting point.

 
APID Agile Protein Interaction DataAnalyzer – http://bioinfow.dep.usal.es/apid/index.htm
 
Ariadne Genomics Pathway Studio – http://www.ariadnegenomics.com/products/pathway-studio
 
BIND Biomolecular Interaction Network Database – http://www.bind.ca
 
 
BioGRID The Biological General Repository for Interaction Datasets – http://www.thebiogrid.org
 
BiologicalNetworks – http://biologicalnetworks.net
 
CellDesigner – http://www.celldesigner.org
 
 
 
DIP Database of Interacting Proteins – http://dip.doe-mbi.ucla.edu/dip/Main.cgi
 
 
GenMAPP Gene Map Annotator and Pathway Profiler – http://www.genmapp.org
 
 
HPRD Human Protein Reference Database – http://www.hprd.org
 
HUBBA Hub objects analyzer – http://hub.iis.sinica.edu.tw/Hubba
 
Ingenuity Systems – http://www.ingenuity.com
 
 
KEGG Kyoto Encyclopedia of Genes and Genomes – http://www.genome.jp/kegg
 
MINT the Molecular INTeraction database – http://mint.bio.uniroma2.it/mint
 
NCI-Nature Pathway Interaction Database – http://pid.nci.nih.gov
 
 
 
 
Pathguide: the pathway resource list – http://www.pathguide.org
 
 
Pathway Commons – http://www.pathwaycommons.org
 
R Project for Statistical Computing – http://www.r-project.org
 
 
SBW Systems Biology Workbench – http://sbw.sourceforge.net
 
TRANSFAC & TRANSPATH – http://www.gene-regulation.com
 
TRED Transcriptional Regulatory Element Database – http://rulai.cshl.edu/cgi-bin/TRED
 
 

Integrating Omics data for signaling pathways, interactome reconstruction, and functional analysis.

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