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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.
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SIM Network Genes Upstream of rpoE
SIM network genes upstream of σ
E response based on SDS/EDTA sensitivity.
Genes marked as confirmed based on testing transcription from the σ
E-controlled rpoH P3-lacZ
(+, partially or fully required; -, not required). Figs. 4J, S8, Table S11
| Class | candidate σE response deficient
(SDS-EDTA-sensitive mutants) | confirmed σE response deficient |
| Cellular processes | acrA | |
| Cellular processes | acrB | |
| Metabolism | apaH | + |
| Regulators | arcA | + |
| Electron transfer | cyoA | + |
| Electron transfer | cyoD | + |
| Metabolism | cysD | |
| Electron transfer | fre | + |
| Regulators | fruR | + |
| Chaperones and proteases | groES | |
| Electron transfer | hemL | + |
| Chaperones and proteases | hfq | |
| Regulators | ihfA | |
| Metabolism | lipB | + |
| Chaperones and proteases | lon | + |
| Regulators | lrp | + |
| Electron transfer | mdh | + |
| Electron transfer | nuoC | + |
| Electron transfer | nuoG | + |
| Electron transfer | nuoH | + |
| Electron transfer | nuoJ | + |
| Electron transfer | nuoK | + |
| Electron transfer | nuoL | + |
| Regulators | nusA | |
| Regulators | phoU | + |
| Regulators | ppk | |
| Cellular processes | pstB | + |
| Cellular processes | pstC | + |
| Regulators | rpoE | + |
| Cellular processes | rppH | + |
| Electron transfer | sdhB | + |
| Electron transfer | sdhD | + |
| Metabolism | speE | |
| Cellular processes | tatC | |
| Cellular processes | trxB | + |
| Electron transfer | ubiA | + |
| Electron transfer | ubiD | + |
| Electron transfer | ubiE | + |
| Electron transfer | ubiH | + |
| Electron transfer | ubiX | + |
| Unknown | ygfA | + |
| Unknown | yigP | + |
| Cellular processes | znuA | |
| Cellular processes | znuC | + |
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Excel versions of supplemental tables:
