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Table 1 Results of Sliding Window approach for identification of differentially expressed fragments regulated by σH

From: An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes

Transcriptional Unit

Genes (strand)

Other genes in the same operon

Number of fragmentsa

σH -dependent promoter (distance from closest gene)

Identified as differentially expressed by standard approachb

1

mpoA (−)

–

1

No

No

2

comGG, comGF,comGB, comGA (−)

comGC, comGD, comGE,

4

Yes (19 nt)

No

3

rpoD,dnaG, LMRG_00908 (−)

–

5

Yes (151 nt)

LMRG_00908

4

comEC,comEA (−)

comEB

7

Yes (22 nt)

comEC, comEA

5

LMRG_02544 (−)

LMRG_02542, LMRG_02543, LMRG_02545

1

No

No

6

LMRG_01010 (−)

LMRG_01009, LMRG_01008,msrA, msrB, LMRG_01005

1

Yes (277 nt)

No

7

coiA (−)

–

1

Yes (81 nt)

coiA

8

lytG (−)

–

2

Yes (220 nt)

lytG

9

LMRG_02194 (−)

LMRG_02196, LMRG_02195, LMRG_02193, LMRG_02192, LMRG_02191, LMRG_02190

1

No

No

  1. a Each fragment is composed of one or more 51 nt overlapping windows
  2. bThis indicates which genes were identified as differentially transcribed with the analysis approach that calculated the normalized RNA-seq coverage for the complete gene (rather than sliding windows) (for full results see Additional file 1: Table S1)