Genes2FANs: connecting genes through functional association networks

BMC Bioinformatics

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.

ISSN: 1471-2105