Rv0195 Transcriptional regulator, LuxR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0195 Transcriptional regulator, LuxR family CDS 230899 231534 + 636 211 TRUE

Rv0195 (Transcriptional regulator, LuxR family) is predicted to be co-regulated in modules bicluster_0447 with residual 0.49 and bicluster_0494 with residual 0.46.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 2,200.00 and 540.00 for bicluster_0447 and 0.68 and 6.50 for bicluster_0494 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 7 of 7
Gene Target Differential Expression Distance Expression pvalue Type
PROBABLE MEMBRANE PROTEIN
Induced 21 1.03 0.000119458 CDS
PROBABLE MEMBRANE PROTEIN
Induced 30 1.03 0.000119458 Internal.TSS
Integral membrane protein, sugar transporter
Repressed -54 -0.8 0.00789052 CDS
ATP binding cassette (ABC) transporter homolog
Induced -140 4.99 0 CDS
Repressed 0 -0.61 0.0263049 Primary.TSS
POSSIBLE SECRETED ALANINE RICH PROTEIN
Induced -44 1.58 0.000000000305 Primary.TSS
Probable forkhead-associated protein
No -70 -0.53 0.0777197 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, MarR family
No -2 -0.22 0.706417 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY LUXR-FAMILY] two component transcriptional regulatory protein
Operon # Operon
135
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
15607336 NP_214709.1 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 GSM1426426 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426427 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426428 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0195_B606 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.690000 1.12

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: 0.512368
p-value INH: 0.860973
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.16 U
D3I 3 3 3.83 12.38 I
D3U 3 3 3.83 12.46 U
D5I 9 5 6.00 11.80 I
D5U 17 5 6.00 11.89 U
D7I 18 7 8.14 12.48 I
D7U 19 7 8.14 12.57 U
D14I 4 14 15.63 11.45 I
D14U 4 14 15.63 12.43 U
D17I 3 17 19.15 9.92 I
D17U 3 17 19.15 12.15 U
D21I 4 21 23.23 9.72 I
D21U 4 21 23.23 12.31 U
D24I 3 24 26.60 8.02 I
D24U 3 24 26.60 12.02 U
D28I 4 28 30.61 8.16 I
D28U 4 28 30.61 11.98 U