Table 3 Multiple biological datasets used for evaluating the performance of CTF
Data type | Data source | Quantity |
|---|---|---|
PINs | DIP, Krogan, and Gavin | DIP: 24,743 interactions among 5093 proteins |
Krogan: 14,317 interactions among 3672 proteins | ||
Gavin: 7669 interactions among 1855 proteins | ||
GO annotations | Saccharomyces GENOME Database (SGD) | 42,878 GO annotations for 7014 proteins |
Gene expression profiles | GEO (Gene Expression Omnibus), GSE3431 series | 36 sample sites for 6777 gene expression sequences |
Subcellular localizations | COMPARTMENTS Database | 4865 proteins involved in 11 different localizations |
Protein complexes | CM270, CM425, CYC408, and CYC428 | 745 protein complexes containing 2167 proteins |
Orthologous information | InParanoid database | 100 genomes (1 prokaryote and 99 eukaryotes) |
Standard essential proteins | MIPS, SGD, DEG, and SGDP Database | 1285 essential proteins, including 1167 in DIP, 929 in Krogan, and 714 in Gavin |