Table_1.xls (21.5 kB)

Intergenic σ54 ChIP-seq peaks.

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posted on 01.10.2015 by Richard P. Bonocora, Carol Smith, Pascal Lapierre, Joseph T. Wade

a Unique ID; OS = Outside of a gene in the Sense orientation, OA = Outside of a gene in the Antisense orientation; each peak is assigned a unique number for cross-referencing with other datasets

b Underlined text indicates that a σ54 has been identified in the homologous position in Salmonella Typhimurium [14]

c Genome coordinate (U00096.2) of ChIP-seq peak center

d FAT = Fold Above Threshold score (indication of ChIP-seq occupancy)

e Associated motif identified using MEME; consensus positions indicated in bold

f Genome coordinate (U00096.2) of motif center

g Genomic orientation of associated motif

h Closest, appropriately oriented, downstream gene (from the predicted transcription start site, 19 bp downstream of the motif center)

i Distance from the predicted transcription start site (19 bp downstream of the motif center) to the start of the closest, appropriately oriented, downstream gene (bp); note that for OS07, the ChIP-seq peak is intergenic but the predicted transcription start site is intragenic

j Position Specific Scoring Matrix (PSSM) score (indication of similarity to the consensus site; see Methods)

k P = Promoter is Predicted in Ecocyc; C = promoter is experimentally Confirmed in Ecocyc [26]

Intergenic σ54 ChIP-seq peaks.