Table 1.
Overview and General Properties of the Data Sets
|
Name of data seta |
Type of functional modules |
Method by which functional modules were determined |
No. of modules |
Average module size |
|---|---|---|---|---|
| Known complexes in Yeast (Mewes et al. 2002; von Mering et al. 2002) | Protein complexes | Manually curated | 126 | 4.36 |
| Known operons in E. coli (Salgado et al. 2001) | Transcriptional modules | Manually curated | 149 | 3.15 |
| EcoCyc metabolic pathways (Karp et al. 2002) | Metabolic pathways | Manually curated | 103 | 4.08 |
| HMS-PCI (Ho et al. 2002) | Protein complexes | High-throughput genomics data | 375 | 5.35 |
| TAP (Gavin et al. 2002) | Protein complexes | High-throughput genomics data | 190 | 7.39 |
| Genes sharing TFB sites (Lee et al. 2002) | Transcriptional modules | High-throughput genomics data | 175 | 5.41 |
| Transcriptional clusters (Ihmels et al. 2002) | Transcriptional modules | Bioinformatics analysis of genomics data | 84 | 33.79 |
| KEGG maps (Ogata et al. 1999) | Metabolic pathways; Protein complexes | Manually curated | 61 | 31.62 |
| Predicted regulons in E. coli (van Nimwegen et al. 2002)
|
Transcriptional modules
|
Bioinformatics analysis of genomics data
|
124
|
10.02
|
-
↵a The data sets were obtained from the Web sites given in their respective publications: See Methods for details.
