Table 1. Overview of the data available in COLOMBOS.
| Strain | Number of genes | Number of contrasts | Missing values (%) | First inclusion | Samples | Experiments | Platforms | |
|---|---|---|---|---|---|---|---|---|
| Escherichia coli | MG1655 | 4321 | 4077 | 3.6 | v1.0 | 5510 | 254 [15] | 73 |
| Bacillus subtilis | 168 | 4176 | 1259 | 3.7 | v1.0 | 1814 | 45 | 35 |
| Salmonella enterica serovar Typhimurium | cross-strain | 6261 | 1066 | 41.6 | v1.0 | 1856 | 36 | 22 |
| LT2 | 4556 | 172 | 6.4 | v2.0 | 316 | 8 | 10 | |
| 14028S | 5416 | 681 | 22.7 | v2.0 | 1252 | 17 | 7 | |
| SL1344 | 4655 | 213 | 9.8 | v2.0 | 288 | 11 | 9 | |
| Streptomyces coelicolor | A3(2) | 8239 | 371 | 7.3 | v2.0 | 546 | 7 [2] | 7 |
| Pseudomonas aeruginosa | PAO1 | 5647 | 559 | 1.6 | v2.0 | 592 | 33 | 2 |
| Helicobacter pylori | 26695 | 1616 | 133 | 3.1 | v2.0 | 256 | 8 | 5 |
| Bacillus anthracis | Ames | 5039 | 66 | 3.0 | v3.0 | 75 | 4 | 4 |
| Bacillus cereus | ATCC 14579 | 5231 | 283 | 2.4 | v3.0 | 392 | 16 | 10 |
| Bacteroides thetaiotaomicron | VPI-5482 | 4816 | 333 | 1.9 | v3.0 | 353 | 19 | 4 |
| Campylobacter jejuni | NCTC 11168 | 1572 | 152 | 12.5 | v3.0 | 260 | 14 | 11 |
| Clostridium acetobutylicum | ATCC 824 | 3778 | 377 | 2.4 | v3.0 | 419 | 12 | 11 |
| Lactobacillus rhamnosus | GG | 2834 | 79 | 3.6 | v3.0 | 158 | 3 | 2 |
| Methanococcus maripaludis | S2 | 1722 | 364 | 1.5 | v3.0 | 728 | 19 | 3 |
| Shigella flexneri | 301 | 4315 | 35 | 17.0 | v3.0 | 38 | 3 | 3 |
| Sinorhizobium meliloti | 1021 | 6218 | 424 | 2.7 | v3.0 | 713 | 20 [19] | 10 |
| Streptococcus pneumoniae | D39 | 1914 | 68 | 5.7 | v3.0 | 136 | 12 | 2 |
| Thermus thermophilus | HB8 | 2173 | 444 | 1.4 | v3.0 | 480 | 6 | 3 |
| Yersinia pestis | CO92 | 3979 | 36 | 6.1 | v3.0 | 72 | 5 | 2 |
Rows of the table represent all the species and strains for which a gene expression compendium is hosted. Columns represent (from left to right): the species name, the strain used as reference genome for microarray probe to gene mapping and RNA-Seq read alignment, the total number of genes in the compendium, the total number of contrasts in the compendium, the percentage of missing values, the COLOMBOS version of the first inclusion of the respective species or strain, the total number of samples from which the compendium's contrasts are built, the total number of corresponding experiments on GEO and ArrayExpress (the latter indicated between square brackets) and the total number of platforms represented.