Tools for pathway/network analysis.
Some resources for protein-protein interactions, pathways and network visualization and
analysis are listed in under ‘Websites used during this workshop” in the ‘Resources for
Functional Modeling’ section.
Additional resources that were not listed/discussed in the workshop are listed below.
Please note that this list is just a primer and not exhaustive. A pathway resource list can
be found here*. Please note that this list is also not exhaustive.
*hyperlink to http://www.pathguide.org/
Multispecies: Integrative Visual Analysis Tool for Biological Networks and
Pathways(http://visant.bu.edu/)
Interactions from Predictome as well as experimentally determined ones by either
directly importing from literatures, or by synchronizing with existing interaction
databases such as Biogrid, MIPS, BIND, HPRD
Plants: Virtual plant (http://virtualplant.bio.nyu.edu/cgi-bin/vpweb2/)
Species: Arabidopsis thaliana, Oryza sativa
Access Gene Ontology, integrated network analysis using Cytoscape
Viruses: VirHostNet (http://pbildb1.univ-lyon1.fr/virhostnet)
Access integrated virus–virus, virus–host and host–host interaction networks
coupled to their functional annotations
Bacteria: Biocyc (http://biocyc.org/)
Multispecies
Collection of 507 Pathway/Genome Databases
Features: Visual analysis of user-supplied omics datasets by painting onto
metabolic map, regulatory map, and genome map
Comparative analysis tools
EcoCyc (http://ecocyc.org/)
Species: Escherichia coli
The EcoCyc project performs literature-based curation of the entire genome, and
of transcriptional regulation, transporters, and metabolic pathways
ProdoNet (http://www.prodonet.tu-bs.de)
Species: Escherichia coli, Bacillus subtilis and Pseudomonas aeruginosa
Visualization tool for regulatory networks from the PRODORIC database
It detects common regulators and metabolic pathways from a list of
genes or proteins
FIVA (http://bioinformatics.biol.rug.nl/standalone/fiva/)
Species: Prokaryotes listed in Uniprot
Can process prokaryotic differential gene expression data for studying regulation
and functional enrichment analysis