Networks for Cancer Genomics Analysis
This page provides direct download to several interaction networks that may be useful in Cancer Genomics Analysis.
Networks are derived from Pathway Commons.
Binary or Pairwise Interaction Networks
Binary or pairwise interaction networks consist of gene nodes and edge interactions only, and do not represent the full semantic complexity of biological pathways.
They can, however, be useful for many different types of network analyses in cancer genomics.
- Binary or pairwise interaction network consisting of interactions derived from HPRD, NCI-Nature Pathway Interaction Database, Reactome, and the MSKCC Cancer Cell Map. The network was constructed as described in Cerami et al., but has since
been updated to reflect current data in Pathway Commons.
- Pathway Commons also provides pairwise interaction networks for individual data sources. They can be downloaded in the Simple Interaction Format (SIF), described in the Pathway Commons README:
BioPax is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data.
Unlike the pairwise interactions above, BioPAX is able to represent the rich biological complexity of multiple types of biological pathways, including
metabolic pathways, molecular interactions, signaling pathways (including molecular states and generics), gene regulation and genetic interactions.
All data from the NCI-Nature Pathway Interaction Database, Reactome, and the MSKCC Cancer Cell Map can be downloaded in BioPAX format:
MSKCC Cell Map
Additional downloads in BioPAX format are available from Pathway Commons.
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RAS/RAF alterations in colorectal cancer
BRCA1 and BRCA2 mutations in ovarian cancer
POLE hotspot mutations in endometrial cancer
Protein changes in PTEN-altered ovarian cancer samples
TP53 and MDM2/4 alterations in GBM
PTEN mutations in GBM in text format
BRAF V600E mutations across cancer types
Patient view of an endometrial cancer case
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