Table 1 |
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|
Data sources for FLN construction |
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|
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 |
|
|
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|
See Additional data file 5 for detailed descriptions of data sources for FLN construction. CC, cellular component; Co-exp, co-expressed; DDI, domain-domain interaction; DS, protein domain sharing; GN, gene neighbor; HPRD, Human Protein Reference Database; Masspec, mass spectrometry; MF, molecular function; MIPS, Munich Information Center for Protein Sequences; PG, phylogenetic profiles; PPI, protein-protein interaction; TexM, text mining; Y2H, yeast two hybrid experiments. |
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Linghu et al. Genome Biology 2009 10:R91 doi:10.1186/gb-2009-10-9-r91 |
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