Rv3328c putative RNA polymerase sigma factor

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3328c sigJ putative RNA polymerase sigma factor CDS 3713394 3714332 - 939 312 FALSE

Rv3328c (putative RNA polymerase sigma factor) is predicted to be co-regulated in modules bicluster_0532 with residual 0.51 and bicluster_0581 with residual 0.61.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.05 for bicluster_0532 and 0.01 and 120.00 for bicluster_0581 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score Re-Annotated Start Tuberculist Annotated Start
-0.573 3714341 3714332
Last update: 10/16/2017 - 15:27
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-18586 MT3431 2627
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No results were found
Motif 1 Motif 2 Residual
bicluster_0532
e.value: 
0.00022
Motif Bicluster: 
e.value: 
0.047
Motif Bicluster: 
0.51
bicluster_0581
e.value: 
0.0065
Motif Bicluster: 
e.value: 
120
Motif Bicluster: 
0.61
Product (LegacyBRC) Product (RefSeq)
PROBABLE ALTERNATIVE RNA POLYMERASE SIGMA FACTOR SIGJ RNA polymerase sigma factor SigJ
Operon # Operon
2173
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

RNA polymerase

17
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15610464 NP_217845.1 Run
GO:0042542

response to hydrogen peroxide

response to hydrogen peroxide

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
GO Category: 
biological_process
3
Total items in this category:  
Description:Expression data from transcription factor over expression experiments. TFOE are matched to the ChIP-seq experiment done simultaneously. This dataset is described in Rustad et al. 2014, Genome Biology.
BioProject Accession GEO Series References Repository Sample Method Sample Type
PRJNA254351 GSM1426982 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426983 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426984 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426982 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426983 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426984 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3328c_B528 UCSC Browser Tracks
Rv3328c_B637 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.570000 0.78

How essentiality calculations were done?

The relative representation of each mutant was determined by calculating the fold change (sequence reads/insertion in cholesterol divided by sequence reads/insertion in glycerol) for each gene. Statistical significance was determined by t-test. Each insertion site in each replicate sample was treated as a separate data point. The hyperbola used for defining genes specifically required for growth in cholesterol was defined by the formula, y = 3.8/x+0.7. Genes above this line are annotated as required for growth on cholesterol.

TRIP log2 fold abundance change

reports the log2 abundance fold change of each TFI strain, relative to no induction, in absence or presence of drug, averaged across experimental replicates. Also reported are the accompanying z-scores and two-sided t-test p-values for each TFI strain under each condition. Please refer to Ma et al., 2020, Nature Microbiology for more information.

p-value Untreated:
p-value INH:
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 8.83 U
D3I 3 3 3.83 15.01 I
D3U 3 3 3.83 15.27 U
D5I 9 5 6.00 I
D5U 17 5 6.00 U
D7I 18 7 8.14 7.54 I
D7U 19 7 8.14 7.31 U
D14I 4 14 15.63 15.15 I
D14U 4 14 15.63 14.15 U
D17I 3 17 19.15 14.54 I
D17U 3 17 19.15 13.55 U
D21I 4 21 23.23 14.77 I
D21U 4 21 23.23 13.71 U
D24I 3 24 26.60 14.22 I
D24U 3 24 26.60 13.08 U
D28I 4 28 30.61 14.48 I
D28U 4 28 30.61 13.29 U