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
•	BioCarta Pathways – http://www.biocarta.com/genes/index.asp
•	BioGRID The Biological General Repository for Interaction Datasets – http://www.thebiogrid.org
•	BiologicalNetworks – http://biologicalnetworks.net
•	CellDesigner – http://www.celldesigner.org
•	ClusterMaker – http://www.cgl.ucsf.edu/cytoscape/cluster/clusterMaker.html
•	Cytoscape – http://www.cytoscape.org
•	DIP Database of Interacting Proteins – http://dip.doe-mbi.ucla.edu/dip/Main.cgi
•	Entrez Gene – http://www.ncbi.nlm.nih.gov/gene
•	GenMAPP Gene Map Annotator and Pathway Profiler – http://www.genmapp.org
•	GraphWeb – http://biit.cs.ut.ee/graphweb
•	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
•	IntAct – http://www.ebi.ac.uk/intact
•	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
•	NetPath – http://www.netpath.org
•	NetworkAnalyzer – http://med.bioinf.mpi-inf.mpg.de/netanalyzer
•	Pajek – http://vlado.fmf.uni-lj.si/pub/networks/pajek
•	Pathguide: the pathway resource list – http://www.pathguide.org
•	PathVisio – http://www.pathvisio.org
•	Pathway Commons – http://www.pathwaycommons.org
•	R Project for Statistical Computing – http://www.r-project.org
•	Reactome – http://www.reactome.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
•	UniProt – http://www.uniprot.org
•	WikiPathways – http://www.wikipathways.org/index.php/WikiPathways

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