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Table 1 Classification of up- or down-regulated 80 genes when YmdB was overexpressed

From: Escherichia coliYmdB regulates biofilm formation independently of its role as an RNase III modulator

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, mqsR 3 , pspB 1,2 , pspC 1,3 , relE 3 , rpoA, rpoB, rpoC, rplD, rpoE 3 , rseB, srlR, yoeB, ygiT 3

20

GO:0006260

GO:0006351

GO:0006352

GO:0006355

GO:0045892

   

GO:0055072

Cellular responses

cspB, cspG, emrA, mprA, nusA, pspB 1,3 , pspC 1,3 , pspD 1,3 ,

13

GO:0006950

GO:0009266

GO:0009271

relE 3 , rplD, rpoE 3 , rseA 3 , sseA

GO:0009408

GO:0009409

   

GO:0046677

Modification

csdA, iscA, iscU, mqsR 3 , pheT,

11

GO:0006432

GO:0016226

relE 3 , srlB 2 , srlE 2

GO:0016310

GO:0090305

 

ydaL 3 , yfhJ, ygdK

  

Translation

mqsR 3 , pheT, rplC, rplD, rpsA, rpsJ, yhbC, relE 3

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

ahpC 3 , 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

yeeZ 3

1

GO:0000166

   

GO:0005524

  1. 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.
  2. 3Gene is related to biofilm formation in literature, even though GO term analysis (http://www.ecocyc.org) did not classify it as such.