Rv2160c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2160c Transcriptional regulator, TetR family CDS 2421662 2422003 - 342 113 TRUE

Rv2160c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0094 with residual 0.41 and bicluster_0590 with residual 0.54.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 320.00 and 1,400.00 for bicluster_0094 and 0.00 and 0.00 for bicluster_0590 respectively.

These modules are enriched for following go terms: carbohydrate derivative metabolic proces..., cell division, cellular component organization, regulation of biological quality .

This gene is found to be for growth on cholesterol.

Mutant available?:

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 33 -0.41 0.999609 CDS
Motif 1 Motif 2 Residual
bicluster_0094
e.value: 
320
Motif Bicluster: 
e.value: 
1400
Motif Bicluster: 
0.41
bicluster_0590
e.value: 
0.000087
Motif Bicluster: 
e.value: 
0.0026
Motif Bicluster: 
0.54
Product (LegacyBRC) Product (RefSeq)
Putative uncharacterized protein
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
15609297 NP_216676.1 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 GSM1426796 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426797 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426798 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426796 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426797 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426798 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2160c_B342 UCSC Browser Tracks
Rv2160c_B402 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.470000 24.64

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: 0.728768
p-value INH: 0.553537
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 9.71 U
D3I 3 3 3.83 9.35 I
D3U 3 3 3.83 8.39 U
D5I 9 5 6.00 9.44 I
D5U 17 5 6.00 9.23 U
D7I 18 7 8.14 9.14 I
D7U 19 7 8.14 8.74 U
D14I 4 14 15.63 8.80 I
D14U 4 14 15.63 8.08 U
D17I 3 17 19.15 8.35 I
D17U 3 17 19.15 7.18 U
D21I 4 21 23.23 8.82 I
D21U 4 21 23.23 7.70 U
D24I 3 24 26.60 8.70 I
D24U 3 24 26.60 6.91 U
D28I 4 28 30.61 8.67 I
D28U 4 28 30.61 7.64 U