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


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.

Linghu et al. Genome Biology 2009 10:R91   doi:10.1186/gb-2009-10-9-r91

Open Data