Table 1.
Overview of the data available in COLOMBOS for the seven expression compendia
| E. coli | B. subtilis | S. enterica srv. Typhimurium | S. coelicolor | P. aeruginosa | M. tuberculosis | H. pylori | |
|---|---|---|---|---|---|---|---|
| Genome refseq id | NC_000913.2 (4 March 2013) | NC_000964.3 (20 August 2012) | NC_003277.1, NC_003197.1 (3 April 2013) | NC_003888.3, NC_003903.1, NC_003904.1 (23 May 2013) | NC_002516.2 (23 May 2013) | NC_000962.3 (15 February 2013) | NC_000915.1 (21 December 2012) |
| Number of genes | 4321 | 4167 | 4560 | 8239 | 5647 | 4068 | 1617 |
| Number of contrasts | 2470 | 723 | 914 | 371 | 482 | 549 | 122 |
| Missing values | 3.11% | 4.54% | 6.42% | 7.35% | 1.53% | 2.81% | 3.09% |
| Source DB | GEO, AE | GEO | GEO, AE | GEO, AE | GEO | GEO | GEO |
| Samples | 3435 | 964 | 1594 | 546 | 511 | 1095 | 244 |
| Experiments | 131 | 21 | 37 | 9 | 29 | 11 | 7 |
| Platforms | 39 | 21 | 22 | 7 | 2 | 11 | 4 |
| External DBs | |||||||
| Pathway | EcoCyc | BioCyc | BioCyc | BioCyc | BioCyc | BioCyc | BioCyc |
| Regulon | RegulonDB | BsubCyc,DBTBS | Galagan et al. (21) | ||||
| Operon | RegulonDB | BioCyc | BioCyc | BioCyc | BioCyc | BioCyc | BioCyc |
| GO | UniProt GOA | UniProt GOA | UniProt GOA | UniProt GOA | UniProt GOA | UniProt GOA | UniProt GOA |