Rv0135c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0135c Transcriptional regulator, TetR family CDS 162644 163249 - 606 201 TRUE

Rv0135c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0366 with residual 0.53 and bicluster_0567 with residual 0.48.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.00 for bicluster_0366 and 200.00 and 6,500.00 for bicluster_0567 respectively.

These modules are enriched for following go terms: hydrolase activity, acting on ester bond... hydro-lyase activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 119
Gene Target Differential Expression Distance Expression pvalue Type
Serine/threonine-protein kinase PknA (EC 2.7.11.1)
No -124 -0.06 0.884138 Primary.TSS
Cell division protein FtsI [Peptidoglycan synthetase] (EC 2.4.1.129)
No -124 -0.13 0.762306 Internal.TSS
Serine/threonine phosphatase PPP (EC 3.1.3.16)
No -6 -0.01 0.973696 Primary.TSS
NA -64 Primary.TSS
Endoglucanase A precursor (EC 3.2.1.4)
No -78 0.47 0.548625 CDS
Oxidoreductase
No -17 -0.26 0.828934 Internal.TSS
Cytochrome P450 138
Repressed -58 -1.49 0.000171088 CDS
MCE-family protein Mce1B
No -52 0.2 0.776736 Antisense.TSS
Aldehyde dehydrogenase (EC 1.2.1.3)
No -104 0.13 0.815286 Antisense.TSS
Transcriptional regulator, TetR family
No 47 -0.43 0.54078 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No 44 -0.07 0.984804 CDS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
95
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
15607277 NP_214649.1 Run
GO:0005886

plasma membrane

plasma membrane

Details: 
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO Category: 
cellular_component
1284
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 GSM1426410 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426411 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426412 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0135c_B398 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.010000 0.40

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: 0.980123
p-value INH: 0.0154749
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.98 U
D3I 3 3 3.83 14.55 I
D3U 3 3 3.83 14.19 U
D5I 9 5 6.00 12.91 I
D5U 17 5 6.00 12.92 U
D7I 18 7 8.14 14.19 I
D7U 19 7 8.14 13.98 U
D14I 4 14 15.63 12.54 I
D14U 4 14 15.63 13.74 U
D17I 3 17 19.15 10.82 I
D17U 3 17 19.15 13.48 U
D21I 4 21 23.23 10.43 I
D21U 4 21 23.23 13.56 U
D24I 3 24 26.60 8.46 I
D24U 3 24 26.60 13.44 U
D28I 4 28 30.61 8.77 I
D28U 4 28 30.61 13.41 U