Table 1.
Classification of up- or down-regulated 80 genes when YmdB was overexpressed
| Functions | Gene | No. of gene | Go term ID |
|---|---|---|---|
|
Transport |
dppA, emrA, exbB, exuT, fdx, fecI, gutM, icd, mntH, nrfA2, proP, srlA2, srlB2, srlE2, srlR, sucA2, sucC2, sucD2, tdcC, tolB, tolR, yhbE, ynfM |
23 |
GO:0006810 |
| GO:0006811 | |||
| GO:0006855 | |||
| GO:0006865 | |||
| GO:0006099 | |||
| GO:0009401 | |||
| GO:0015031 | |||
| GO:0015992 | |||
| GO:0017038 | |||
| GO:0022900 | |||
| GO:0043213 | |||
| |
|
|
GO:0055085 |
|
Transcription/replication |
cspB, cspG, fecI, gutM, lacI, mprA, mukF, mqsR3, pspB1,2, pspC1,3, relE3, rpoA, rpoB, rpoC, rplD, rpoE3, rseB, srlR, yoeB, ygiT3 |
20 |
GO:0006260 |
| GO:0006351 | |||
| GO:0006352 | |||
| GO:0006355 | |||
| GO:0045892 | |||
| |
|
|
GO:0055072 |
|
Cellular responses |
cspB, cspG, emrA, mprA, nusA, pspB1,3, pspC1,3, pspD1,3, |
13 |
GO:0006950 |
| GO:0009266 | |||
| GO:0009271 | |||
|
relE3, rplD, rpoE3,rseA3, sseA |
GO:0009408 |
||
| GO:0009409 | |||
| |
|
|
GO:0046677 |
|
Modification |
csdA, iscA, iscU, mqsR3, pheT, |
11 |
GO:0006432 |
| GO:0016226 | |||
|
relE3, srlB
2
, srlE
2
| |||
| GO:0016310 | |||
| GO:0090305 | |||
| |
ydaL3, yfhJ, ygdK |
|
|
|
Translation |
mqsR3, pheT, rplC, rplD, rpsA, rpsJ, yhbC, relE3 |
8 |
GO:0006412 |
| GO:0017148 | |||
|
Metabolic process |
fabD, lacI, srlA
2
, srlB
2
, srlD
2
, srlE
2
, sucA
2
, ycjM |
8 |
GO:0008152 |
|
Oxidation-reduction |
ahpC3, nrfA
2
, srlD
2
, sucA
2
, torZ, ygjR |
6 |
GO:0055114 |
|
Biosynthesis |
fabD |
1 |
GO:0006633 |
| GO:0006654 | |||
| |
|
|
GO:0008610 |
|
Cell cycle |
mukF |
1 |
GO:0007049 |
| |
|
|
GO:0051301 |
|
Nucleotide binding |
yeeZ3 |
1 |
GO:0000166 |
| GO:0005524 |
Genes 1up- (>3-fold) or 2down-(<0.5-fold) regulated by YmdB overexpression were indicated. Detailed quantitative data are shown in Additional file 1: Table S3.
3Gene is related to biofilm formation in literature, even though GO term analysis (http://www.ecocyc.org) did not classify it as such.