Rv3160c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3160c Transcriptional regulator, TetR family CDS 3529338 3529979 - 642 213 TRUE

Rv3160c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0078 with residual 0.48 and bicluster_0239 with residual 0.41.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 360.00 and 14,000.00 for bicluster_0078 and 2,700.00 and 6,000.00 for bicluster_0239 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15064 MT3249 2611
Displaying 1 - 10 of 14
Gene Target Differential Expression Distance Expression pvalue Type
No -63 0.19 0.999974 CDS
No -22 -0.24 0.999974 CDS
Probable phiRV1 phage protein
No -38 -0.29 0.999974 CDS
No -68 -0.11 0.999974 Primary.TSS
PE family protein
No -13 -0.1 0.999974 Primary.TSS
FIG055075: Possibly a cell division protein, antigen 84 in Mycobacteria
No 38 0.21 0.999974 Primary.TSS
No -149 -0.26 0.999974 CDS
Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit
Repressed -15 -2.85 2.56e-19 Primary.TSS
DNA-directed RNA polymerase alpha subunit (EC 2.7.7.6)
No 53 0.08 0.999974 Primary.TSS
SSU ribosomal protein S4p (S9e)
No 53 0.16 0.999974 Internal.TSS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
WhiB family transcriptional regulator
Repressed 11 -0.7 0.0408141 Primary.TSS
putative two-component system response regulator
No 29 0.5 0.286227 Primary.TSS
No 26 0.19 0.662728 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY TETR-FAMILY] TetR family transcriptional regulator
Operon # Operon
2060 -
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
15610296 NP_217676.1 Run
GO:0010033

response to organic substance

response to organic substance

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 an organic substance stimulus.
GO Category: 
biological_process
8
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 GSM1426930 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426931 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426932 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3160c_B240 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.720000 1.65

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: 0.125073
p-value INH: 0.366556
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.68 U
D14I 4 14 15.63 12.07 I
D14U 4 14 15.63 11.46 U
D17I 3 17 19.15 11.96 I
D17U 3 17 19.15 11.45 U
D21I 4 21 23.23 11.83 I
D21U 4 21 23.23 11.46 U
D24I 3 24 26.60 11.45 I
D24U 3 24 26.60 11.18 U
D28I 4 28 30.61 11.35 I
D28U 4 28 30.61 11.03 U
D3I 3 3 3.83 11.95 I
D3U 3 3 3.83 11.24 U
D5I 9 5 6.00 12.43 I
D5U 17 5 6.00 12.15 U
D7I 18 7 8.14 11.82 I
D7U 19 7 8.14 11.50 U