Collections of regulogs classified by taxonomic group
Each taxonomy collection organizes all reconstructed regulogs for a given set of taxonomically related microbial genomes. The taxonomy collections represent results of large-scale reconstruction of regulon operated by either transcription factors or RNA regulatory elements. The taxonomical collections of regulons are valuable for modeling the evolution of transcriptional regulatory networks and could be used as a framework for interpretation of high-throughput gene expression data.
| Reconstructed | Studied | |||
|---|---|---|---|---|
| Taxonomic group | TF regulogs (regulons) | RNA regulogs (regulons) | Total regulogs (regulons) | Genomes |
| Alcaligenaceae | 25 (60) | 0 (0) | 25 (60) | 3 |
| Alteromonadales | 50 (231) | 3 (13) | 53 (244) | 9 |
| Archaeoglobales | 2 (6) | 0 (0) | 2 (6) | 3 |
| Bacillales | 154 (901) | 39 (358) | 193 (1259) | 11 |
| Bacteroidaceae | 38 (223) | 2 (22) | 40 (245) | 11 |
| Bifidobacteriaceae | 68 (299) | 2 (18) | 70 (317) | 10 |
| Burkholderia | 75 (375) | 9 (67) | 84 (442) | 8 |
| Campylobacteraceae | 0 (0) | 2 (4) | 2 (4) | 9 |
| Caulobacterales | 33 (100) | 8 (26) | 41 (126) | 4 |
| Chlamydiales | 4 (21) | 0 (0) | 4 (21) | 7 |
| Chlorobiales | 5 (46) | 6 (45) | 11 (91) | 11 |
| Chloroflexi | 30 (107) | 17 (65) | 47 (172) | 5 |
| Clostridia-1 | 33 (160) | 0 (0) | 33 (160) | 8 |
| Clostridia-2 | 19 (40) | 1 (3) | 20 (43) | 3 |
| Clostridia-3 | 19 (190) | 2 (28) | 21 (218) | 14 |
| Clostridiaceae | 0 (0) | 40 (566) | 40 (566) | 20 |
| Comamonadaceae | 72 (316) | 4 (26) | 76 (342) | 11 |
| Corynebacteriaceae | 59 (262) | 13 (56) | 72 (318) | 8 |
| Cyanobacteria | 19 (182) | 11 (64) | 30 (246) | 14 |
| Deinococcus-Thermus | 10 (29) | 13 (44) | 23 (73) | 5 |
| Desulfovibrionales | 101 (428) | 9 (43) | 110 (471) | 10 |
| Desulfuromonadales | 19 (111) | 3 (18) | 22 (129) | 9 |
| Enterobacteriales | 127 (812) | 18 (147) | 145 (959) | 12 |
| Enterococcaceae | 15 (24) | 0 (0) | 15 (24) | 2 |
| Flavobacteria | 4 (10) | 0 (0) | 4 (10) | 19 |
| Francisellaceae | 2 (4) | 3 (6) | 5 (10) | 3 |
| Frankineae/Propionibacterineae/Pseudonocardiaceae | 29 (123) | 0 (0) | 29 (123) | 9 |
| Halobacteriales | 3 (32) | 0 (0) | 3 (32) | 11 |
| Helicobacteraceae | 0 (0) | 2 (3) | 2 (3) | 8 |
| Lactobacillaceae | 82 (485) | 39 (409) | 121 (894) | 15 |
| Listeriaceae | 25 (94) | 0 (0) | 25 (94) | 4 |
| Methanobacteriales | 1 (5) | 0 (0) | 1 (5) | 5 |
| Methanococcales | 0 (0) | 0 (0) | 0 (0) | 0 |
| Methanomicrobiales | 2 (10) | 0 (0) | 2 (10) | 5 |
| Methanosarcinales | 2 (9) | 0 (0) | 2 (9) | 6 |
| Micrococcineae | 40 (220) | 0 (0) | 40 (220) | 14 |
| Moraxellaceae | 29 (58) | 4 (8) | 33 (66) | 4 |
| Mycobacteriaceae | 30 (154) | 12 (80) | 42 (234) | 9 |
| Nocardiaceae | 35 (114) | 0 (0) | 35 (114) | 4 |
| Oceanospirillales/Alteromonadales | 72 (247) | 3 (16) | 75 (263) | 12 |
| Pasteurellales | 31 (181) | 11 (82) | 42 (263) | 9 |
| Planctomycetes | 2 (9) | 0 (0) | 2 (9) | 5 |
| Pseudomonadaceae | 71 (338) | 9 (58) | 80 (396) | 8 |
| Psychromonadaceae/Aeromonadales | 56 (194) | 3 (16) | 59 (210) | 6 |
| Ralstonia | 69 (277) | 10 (46) | 79 (323) | 6 |
| Rhizobiales | 97 (539) | 12 (124) | 109 (663) | 15 |
| Rhodobacterales | 76 (386) | 13 (115) | 89 (501) | 15 |
| Rhodospirillales | 40 (154) | 3 (14) | 43 (168) | 9 |
| Shewanellaceae | 90 (911) | 15 (214) | 105 (1125) | 16 |
| Sphingobacteria | 6 (14) | 0 (0) | 6 (14) | 8 |
| Sphingomonadales | 28 (108) | 2 (7) | 30 (115) | 7 |
| Staphylococcaceae | 52 (281) | 29 (194) | 81 (475) | 7 |
| Streptococcaceae | 70 (595) | 29 (330) | 99 (925) | 15 |
| Streptococcus | 0 (0) | 0 (0) | 0 (0) | 0 |
| Streptomycetaceae | 36 (120) | 3 (8) | 39 (128) | 4 |
| Sulfolobales | 3 (15) | 0 (0) | 3 (15) | 5 |
| Thermoanaerobacterales | 16 (71) | 3 (19) | 19 (90) | 7 |
| Thermococcales | 4 (28) | 0 (0) | 4 (28) | 7 |
| Thermoproteales | 3 (14) | 0 (0) | 3 (14) | 5 |
| Thermotogales | 34 (245) | 13 (74) | 47 (319) | 11 |
| Various betaproteobacteria | 47 (158) | 4 (24) | 51 (182) | 12 |
| Vibrionales | 70 (444) | 17 (140) | 87 (584) | 10 |
| Xanthomonadales | 42 (106) | 4 (10) | 46 (116) | 4 |