Network · genome-wide
Every regulator we have data for
The core circuit is curated from the literature. This view is computed: 33 regulators and 8,627 links to 3,173 genes, built by applying one set of stated rules to the binding and expression data in the genome browser. Each link carries its grade of evidence, so you can tell a promoter that is both bound and responsive from one that is only bound.
bound and responsive (159) · bound only (6,373) · responsive only, may be indirect (2,095)
Who regulates the regulators
Regulators linked to each other through the same rules. 84 feed-forward loops appear among the bound links, where one regulator acts on a target both directly and through a second regulator. Select a regulator to open its regulon below; regulators whose own gene could not be confirmed have no incoming links.
This view needs JavaScript; the table of regulators below lists the same counts.
Regulons
Cell-cycle master regulators
DNA methylation
Development and surfaces
Sigma factors and RNA polymerase
Growth
Stress and DNA damage
Nutrients
Metals
Choose a regulator, or search for a gene.
Cell-cycle clock
The 486 genes whose start sites Zhou et al. (2015) found to be cell-cycle regulated, placed around the cycle by when their RNA peaks across five sampled stages (Fang et al. 2013), further out the more their level swings. Colour shows which master regulator binds the promoter. Selecting a regulator above lights up its own targets here. Phases are approximate: five samples per cycle.
Shared targets
How much any two regulators' bound targets overlap (Jaccard index), for regulators with at least ten bound targets. Large overlaps flag regulators that act on the same promoters: partners, competitors, or factors that travel with RNA polymerase. Select a cell to list the shared genes.
How it was built
Promoters. A gene's promoter runs from 200 bp upstream of each primary start site mapped by Zhou et al. (2015) to its start codon (at least 50 bp downstream). Genes without a mapped start site get 300 bp upstream of the start codon, marked "inferred". Genes later in an operon (Schrader et al. 2014) share the first gene's promoter, and keep their own when they have one.
Binding. A regulator binds a promoter when a peak summit falls in it. Where the authors published peak calls, those are used; tables that report fold enrichment keep peaks of at least 2-fold. Where only coverage was deposited, Caulobase calls peaks with one rule for every factor: windows at least 4 times the genome-wide median and in the top 0.5% of windows, merged across gaps up to 100 bp, spanning at least 2 windows.
Response. A gene responds when its level changes at least 2-fold in an array where the regulator was deleted or depleted (or, for SciP, also overexpressed). A gene that falls without the regulator counts as activated by it. Responses alone may be indirect.
What this is not. Binding is not proof of regulation, and a missing link is not proof of none: data exist for some regulators and conditions only. Some curated links, such as CtrA repressing gcrA, do not appear because no peak falls at that promoter in these datasets. The computed network is tested against links established independently (CtrA at ccrM, ctrA, sciP, pilA and ftsQ; LexA at lexA, recA and sidA; PhoB at pst; SciP repressing flagellar genes), and the build fails if any is lost. The whole network can be downloaded as genome-network.json.
Regulators and their data
| Regulator | Gene | Bound + resp. | Bound | Resp. only | Data |
|---|---|---|---|---|---|
| CtrA | CCNA_03130 | 0 | 601 | 0 | authors' peaks (295 peaks): Fumeaux et al. 2014 GSE52849 (GSM1277021) authors' peaks (295 peaks): Delaby et al. 2019 GSE134017 (GSM3933392) |
| GcrA | CCNA_02328 | 1 | 223 | 48 | Caulobase peak calls on authors' coverage (79 peaks): Haakonsen et al. 2015 GSE73925 (GSM1906338) expression without the regulator: Holtzendorff et al. 2004 GSE1135 |
| SciP | CCNA_00948 | 62 | 302 | 217 | authors' peaks (331 peaks): Fumeaux et al. 2014 GSE52849 (GSM1277022) expression without the regulator: Gora et al. 2010 GSE22062 expression with extra regulator: Gora et al. 2010 GSE22062 |
| MucR1 | CCNA_00982 | 0 | 187 | 0 | authors' peaks (160 peaks): Fumeaux et al. 2014 GSE52849 (GSM1277024) |
| MucR2 | CCNA_00998 | 0 | 151 | 0 | authors' peaks (225 peaks): Fumeaux et al. 2014 GSE52849 (GSM1277025) |
| CcrM | CCNA_00382 | 0 | 0 | 169 | expression without the regulator: Gonzalez et al. 2014 GSE52375 |
| FlbD | CCNA_00954 | 0 | 54 | 0 | authors' peaks (21 peaks): Fumeaux et al. 2014 GSE52849 (GSM1277023) |
| TacA | CCNA_03424 | 0 | 76 | 0 | Caulobase peak calls on authors' coverage (31 peaks): Janakiraman et al. 2016 GSE85186 (GSM2259919) |
| TipR | CCNA_00852 | 0 | 8 | 0 | Caulobase peak calls on authors' coverage (4 peaks): Costafrolaz et al. 2023 GSE225487 (GSM7049355) |
| RtrA | CCNA_03267 | 0 | 883 | 0 | authors' peaks (1294 peaks): McLaughlin et al. 2023 GSE241053 |
| RtrB | CCNA_02415 | 0 | 605 | 0 | authors' peaks (691 peaks): McLaughlin et al. 2023 GSE241053 |
| RtrC | — | 0 | 313 | 0 | authors' peaks (297 peaks): McLaughlin et al. 2022 GSE201497 |
| CdxA | — | 0 | 672 | 0 | authors' peaks (923 peaks): McLaughlin et al. 2023 GSE241053 |
| CdxB | — | 0 | 212 | 0 | authors' peaks (251 peaks): McLaughlin et al. 2023 GSE241053 |
| RedN | — | 0 | 32 | 0 | Caulobase peak calls on authors' coverage (42 peaks): Arias‐Cartin et al. 2016 GSE85344 (GSM2265434) |
| σ32 | CCNA_03195 | 0 | 179 | 0 | Caulobase peak calls on authors' coverage (76 peaks): Haakonsen et al. 2015 GSE73925 (GSM1906341) |
| σ54 | CCNA_03713 | 0 | 81 | 0 | Caulobase peak calls on authors' coverage (50 peaks): Haakonsen et al. 2015 GSE73925 (GSM1906342) |
| σT | CCNA_03589 | 0 | 0 | 171 | expression without the regulator: Lourenço et al. 2011 GSE26977 |
| TrcR | CCNA_03401 | 0 | 774 | 0 | authors' peaks (525 peaks): Delaby et al. 2021 GSE148652 (GSM4476143) |
| CdnL | CCNA_00690 | 96 | 217 | 1308 | Caulobase peak calls on authors' coverage (112 peaks): Smith et al. 2024 GSE249185 (GSM7927858) expression without the regulator: Woldemeskel et al. 2020 GSE139873 |
| LexA | CCNA_01979 | 0 | 103 | 0 | authors' peaks (64 peaks): Kirkpatrick et al. 2016 GSE76721 (GSM2036554) |
| HigA | CCNA_03132 | 0 | 123 | 0 | authors' peaks (588 peaks): Kirkpatrick et al. 2016 GSE76721 (GSM2036555) |
| HigX | — | 0 | 178 | 0 | authors' peaks (137 peaks): Brejndal et al. 2026 GSE310922 (GSM9312241) |
| DriD | — | 0 | 23 | 0 | Caulobase peak calls on authors' coverage (23 peaks): Gozzi et al. 2022 GSE197978 (GSM5935095) |
| RogA | — | 0 | 35 | 0 | Caulobase peak calls on authors' coverage (19 peaks): Gozzi et al. 2022 GSE184477 (GSM5589677) |
| PhoB | CCNA_00296 | 0 | 143 | 0 | Caulobase peak calls on authors' coverage (79 peaks): Lubin et al. 2016 GSE71860 (GSM1847008) |
| NtrC | CCNA_01815 | 0 | 21 | 0 | Caulobase peak calls on authors' coverage (7 peaks): North et al. 2023 GSE234096 |
| NtrX | CCNA_01817 | 0 | 6 | 0 | Caulobase peak calls on authors' coverage (2 peaks): Vogt et al. 2024 GSE247928 (GSM7903192) |
| ChvI | CCNA_00237 | 0 | 114 | 0 | Caulobase peak calls on authors' coverage (87 peaks): Costafrolaz et al. 2026 GSE309018 (GSM9258338) |
| KdpE | CCNA_01667 | 0 | 25 | 0 | authors' peaks (20 peaks): Quintero-Yanes et al. 2024 GSE253227 (GSM8381837) |
| UzcR | CCNA_02845 | 0 | 32 | 0 | Caulobase peak calls on authors' coverage (14 peaks): Park et al. 2017 GSE87171 (GSM2323851) |
| Fur | CCNA_00055 | 0 | 0 | 147 | expression without the regulator: da Silva Neto et al. 2013 GSE45653 |
| Zur | CCNA_00362 | 0 | 0 | 35 | expression without the regulator: Mazzon et al. 2014 GSE57136 |