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.