Table 1

FAN properties
Network Scoring Method Network Cutoff Data Source Nodes Edges
CMAP co-expression Binomial Proportion* 130 Connectivity Map Database 8,924 62,382
Transcription Factors (ChIP-X) Binomial Proportion* 27 ChEA database 13,223 70,347
GeneRIF Binomial Proportion* 2000 NCBI GeneRIF 3,777 27,487
GO Molecular Function Binomial Proportion* 160 Gene Ontology 2,944 23,356
TRANSFAC Binomial Proportion 27 TRANSFAC 15,252 94,642
GeneSigDB Binomial Proportion 350 GeneSigDB 10,536 65,776
MicroRNA Jaccard* 0.3 TargetScan 6,590 46,161
Mouse Phenotype Jaccard* 0.5 MGI MP Browser 7,553 52,637
Metabolites Jaccard* 0.35 Human Metabolome Database 3,577 28,617
Structural Domains Jaccard* 0.5 Pfam and InterPro 6,746 46,463
GO Biological Process Jaccard* 0.99 Gene Ontology 4,287 29,988
OMIM Expanded Jaccard 0.99 OMIM Morbid Map 2,051 23,191
OMIM Disease Jaccard 0.99 OMIM Morbid Map 1,618 22,643
Drug Target Jaccard 0.5 DrugBank 2,121 16,807
PPI None N/A 13 Databases 15,548 64,741

Properties of all the FANs along with their scoring method, scoring cutoff, data source, edge and node totals. * indicates that the declustering method was applied.

Dannenfelser et al.

Dannenfelser et al. BMC Bioinformatics 2012 13:156   doi:10.1186/1471-2105-13-156

Open Data