Table 1 Data sources for FLN construction
Data sources | Description | Number of unique gene pairs | Number of unique genes |
|---|---|---|---|
Curated PPI | Curated human PPI from HPRD, BIND, BIOGRID, INTACT, MIPS, DIPS, and MINT [45–51] | 90,352 | 10,281 |
Y2H | PPI from high-throughput yeast two-hybrid experiments [52] | 2,611 | 1,522 |
Masspec | PPI from large-scale mass spectrometry experiments [53] | 2,046 | 1,159 |
DDI | Protein pairs containing interacting protein domains [38, 39] | 6,933,469 | 13,454 |
Co-exp | Expression correlation from multiple large-scale expression datasets [56, 88–90] | 5,110,798 | 16,287 |
DS | Proteins pairs sharing same protein domains [91] | 2,064,262 | 17,328 |
PG | Gene pairs having correlated phylogenetic profiles [56] | 18,086 | 2,607 |
GN | Gene pairs located close to each other along the chromosome [56] | 10,070 | 1,365 |
Fusion | Protein pairs fused into one single protein in other species [56] | 361 | 361 |
Yeast | Functional associations mapped from seven types of functional genomics data in yeast through gene orthology [92] | 123,380 | 3,809 |
Worm | Functional associations mapped from four types of functional genomics data in worm through gene orthology [41] | 96,911 | 5,737 |
Fly | Functional associations mapped from three types of functional genomics data in fly through gene orthology [56] | 139,984 | 5,966 |
Mouse-rat | Functional associations mapped from three types of functional genomics data in mouse and rat through gene orthology [56] | 254,477 | 11,789 |
TexM | Co-occurrence in PubMed abstracts [56] | 518,716 | 12,286 |
MF | Gene pairs sharing same molecular function terms in GO [93] | 6,937,725 | 7,863 |
CC | Gene pairs sharing same cellular component terms in GO [93] | 5,591,796 | 12,503 |