funcoup_cancer — Human functional gene coupling network (2014)
- Description
A global network of functional couplings between human genes, used by S. K. Merid, D. Goranskaya and A. Alexeyenko for the network enrichment analysis of somatic mutations in glioblastoma and ovarian cancer genomes (named
merged6_and_wir1_HC2by the authors). Nodes represent genes (or their protein products), and an undirected edge between two genes means that they are predicted or known to be functionally coupled, e.g. by physical interaction, membership in the same pathway or protein complex, or regulation. The network was built by merging a higher-confidence version (FClim_HC2) of the FunCoup network, which integrates diverse high-throughput evidence (e.g. protein interactions, co-expression, sub-cellular co-localization) from human and other eukaryotes via orthologs, with curated functional links from CORUM (protein complex membership), PhosphoSite (kinase-substrate pairs), KEGG (pathways and protein complexes) and MSigDB (pairs of genes regulated by the same transcription factor), and with a network of regulatory links reverse-engineered by the authors from cancer data (wir1). Among the networks benchmarked by the authors, this one best recovered known members of cancer-related gene sets. The types, origins and confidence of the links are not included in the distributed file. The network contains self-loops (genes coupled to themselves, as given in the source data).The network has the following properties:
- Nodes:
name, the gene symbol, in lower case (as in the source data; the symbol of SEPT11 appears in the date-converted form "11-sep").1
- Nodes:
- Tags
- Biological Protein interactions Unweighted
- Citation
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- S. K. Merid, D. Goranskaya, A. Alexeyenko, "Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis." BMC Bioinformatics 15, 308 (2014) 10.1186/1471-2105-15-308 Sci-Hub
- Upstream URL OK
- https://web.archive.org/web/20240415205044/https://research.scilifelab.se/andrey_alexeyenko/downloads/test_data/merged6_and_wir1_HC2
- Networks
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Tip: hover over a column header for a description.
Column legend
- $\left<k\right>$
- Mean degree
- $\sigma_k$
- Standard deviation of the degrees
- $\lambda_h$
- Largest eigenvalue of the Hashimoto (non-backtracking) matrix
- $\tau$
- Random walk mixing time
- $r$
- Degree assortativity
- $c$
- Global clustering coefficient
- $\oslash$
- (Pseudo-) diameter
- $S$
- Relative size of the largest component
- NPs
- Node properties
- EPs
- Edge properties