We are still making minor changes. Feel free to use the browser, but be sure to check back later too
Browse and analyze data from Al Mamun et al. (Science 2012) Identity and Function of a Large Gene Network Underlying Mutagenic Repair of DNA Breaks 338:1344-1348
This dataset of 93 genes was constructed by screening E. coli for mutants deficient in mutagenic repair of DNA breaks under stress, followed by secondary screens for genes that participate in activation of stress responses. This study identifies a network of genes involved in stress-induced mutagenesis (the SIM Network). This data browser allows you to examine the classification of SIM network genes and explore the data from different assays on individual network genes. You can also download excel versions of the supplemental tables from the paper.
Views
- All SIM network genes
- SIM network genes upstream of rpoE
- SIM network genes upstream of rpoS
- UV-sensitive SIM network genes upstream of the SOS response
- Essential SIM network genes and promoter mutations
All SIM Network Genes
| Class | Stress-induced mutagenesis-deficient mutant genes |
|---|---|
| Cellular processes | acrA |
| Cellular processes | acrB |
| Unknown | apaG |
| Metabolism | apaH |
| Regulators | arcA |
| Metabolism | argD |
| Regulators | argR |
| Regulators | barA |
| Regulators | crp |
| Chaperones and proteases | cspC |
| Regulators | cyaA |
| Electron transfer | cyoA |
| Electron transfer | cyoD |
| Metabolism | cysD |
| DNA replication and repair | dinB |
| Cellular processes | dsbA |
| Cellular processes | dsbC |
| Electron transfer | fre |
| Regulators | fruR |
| Regulators | glnK |
| Chaperones and proteases | groES |
| Regulators | hdfR |
| Electron transfer | hemL |
| Chaperones and proteases | hfq |
| Electron transfer | hscB |
| Regulators | ihfA |
| Chaperones and proteases | ldcA |
| Regulators | lexA |
| DNA replication and repair-related | ligA |
| Metabolism | lipB |
| Chaperones and proteases | lon |
| Regulators | lrp |
| Regulators | malI |
| Electron transfer | mdh |
| Regulators | metJ |
| Regulators | nagC |
| Electron transfer | nuoC |
| Electron transfer | nuoG |
| Electron transfer | nuoH |
| Electron transfer | nuoJ |
| Electron transfer | nuoK |
| Electron transfer | nuoL |
| Regulators | nusA |
| Chaperones and proteases | pepP |
| Electron transfer | pgi |
| Metabolism | pgl |
| Regulators | phoU |
| DNA replication and repair | polB |
| Regulators | ppk |
| Chaperones and proteases | prc |
| Cellular processes | proL |
| Cellular processes | pstB |
| Cellular processes | pstC |
| Metabolism | rbsK |
| DNA replication and repair | recA |
| DNA replication and repair | recB |
| DNA replication and repair | recC |
| DNA replication and repair | recF |
| Regulators | rpoE |
| Regulators | rpoS |
| Cellular processes | rppH |
| DNA replication and repair | ruvA |
| DNA replication and repair | ruvB |
| DNA replication and repair | ruvC |
| Electron transfer | sdhB |
| Electron transfer | sdhD |
| Metabolism | speD |
| Metabolism | speE |
| Cellular processes | srlA |
| DNA replication and repair | sulA |
| Cellular processes | tatC |
| Regulators | treR |
| Cellular processes | trxB |
| Electron transfer | ubiA |
| Electron transfer | ubiD |
| Electron transfer | ubiE |
| Electron transfer | ubiH |
| Electron transfer | ubiX |
| DNA replication and repair | umuC |
| Regulators | uvrY |
| Unknown | ybjT |
| Unknown | yfjL |
| Unknown | ygfA |
| Unknown | yhhK |
| Unknown | yicC |
| Unknown | yifE |
| Unknown | yigP |
| Unknown | yjcC |
| Unknown | yqgE |
| Unknown | yqiC |
| Unknown | ytjB |
| Cellular processes | znuA |
| Cellular processes | znuC |
| Class | Stress-induced mutagenesis-deficient mutant genes |
Help
Back to topComing soon...
Download data files
Back to topExcel versions of supplemental tables:
- Table S03. Stress-induced mutation rates of previously unpublished SIM network mutants in quantitative assay.xlsx
- Table S08. sigmaS activity of catalase-defective mutants.xlsx
- Table S02. Genes of the stress-induced-mutagenesis network.xlsx
- Table S09. Upregulating sigmaS via arcB, arcA or rssB mutations partially restores SIM-proficiency to electron transfer mutants.xlsx
- Table S04. Escherichia coli strains and plasmid used.xlsx
- Table S10. RpoS acts in the same pathway (is epistatic with) electron transfer mutations in DSB-dependent SIM.xlsx
- Table S01. Summary of stress-induced-mutagenesis network genetic analyses.xlsx
- Table S05. Validation of SIM network mutants by Tet and Nal mutation assays.xlsx
- Table S11. sigmaE activity of SDS-EDTA-sensitive mutants.xlsx
- Table S06. Correlations of the magnitudes of SIM-deficiency in four stress-induced mutation assays.xlsx