Rv0158 Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0158 Transcriptional regulator, TetR family CDS 186785 187429 + 645 214 TRUE

Rv0158 (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0167 with residual 0.51 and bicluster_0350 with residual 0.37.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 49.00 for bicluster_0167 and 1,000.00 and 4,000.00 for bicluster_0350 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 6 of 6
Gene Target Differential Expression Distance Expression pvalue Type
No -117 0.4 0.687426 Primary.TSS
Malonyl CoA-acyl carrier protein transacylase (EC 2.3.1.39)
No -97 0.06 0.952124 CDS
No -83 -0.81 0.608524 CDS
Type VII secretion integral membrane protein EccD
No -65 0.02 0.957695 Primary.TSS
Transcriptional regulator, ArsR family
No 33 -0.18 0.912567 CDS
No -119 -0.46 0.701875 CDS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
Two component transcriptional regulatory protein DevR
No -51 -0.56 0.00739666 Primary.TSS
Transcriptional regulator, MarR family
Repressed 13 -1.24 0.000249174 Primary.TSS
Transcriptional regulator kstR (Rv3574), TetR family
Repressed -75 -0.64 0.027632 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN [POSSIBLY TETR-FAMILY] TetR family transcriptional regulator
Operon # Operon
113
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

not assigned to any KEGG Pathway.
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15607300 NP_214672.1 Run
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 GSM1426417 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426418 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426419 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426417 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426418 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426419 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0158_B258 UCSC Browser Tracks
Rv0158_B292 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.610000 2.11

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: 0.0000106933
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.80 U
D3I 3 3 3.83 12.77 I
D3U 3 3 3.83 12.41 U
D5I 9 5 6.00 12.89 I
D5U 17 5 6.00 12.52 U
D7I 18 7 8.14 13.92 I
D7U 19 7 8.14 13.05 U
D14I 4 14 15.63 13.69 I
D14U 4 14 15.63 12.56 U
D17I 3 17 19.15 13.68 I
D17U 3 17 19.15 12.25 U
D21I 4 21 23.23 13.78 I
D21U 4 21 23.23 12.40 U
D24I 3 24 26.60 13.65 I
D24U 3 24 26.60 11.87 U
D28I 4 28 30.61 13.78 I
D28U 4 28 30.61 12.09 U