Rv0081 transcriptional regulator, ArsR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0081 transcriptional regulator, ArsR family CDS 89575 89919 + 345 114 TRUE

Rv0081 (transcriptional regulator, ArsR family) is predicted to be co-regulated in modules bicluster_0143 with residual 0.53 and bicluster_0391 with residual 0.53.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 130.00 for bicluster_0143 and 0.00 and 0.00 for bicluster_0391 respectively.

These modules are enriched for following go terms: cellular respiration, energy derivation by oxidation of organi..., generation of precursor metabolites and ..., oxidation-reduction process, NADH dehydrogenase activity, oxidoreductase activity, acting on NAD(P..., oxidoreductase activity, acting on NAD(P... .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 11/20/2020 - 12:11
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15116 MT0088 965
Displaying 1 - 10 of 352
Gene Target Differential Expression Distance Expression pvalue Type
Transcriptional regulator, GntR family
No -17 0.1 0.578812 CDS
Hydrolase
No 3 0.52 0.000921846 Primary.TSS
No 56 0.55 0.000112543 Internal.TSS
No -94 0.55 0.000112543 Internal.TSS
Replicative DNA helicase (EC 3.6.1.-) @ intein-containing
No -94 0.58 0.000000131 Primary.TSS
Cystathionine beta-lyase, type II (EC 4.4.1.8)
No 17 -0.23 0.104976 CDS
PROBABLE MEMBRANE PROTEIN
Induced 59 0.84 0.000000185 Antisense.TSS
Formate hydrogenlyase subunit 11
Repressed -1 -2.54 9.17e-24 Primary.TSS
Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
No -129 0.26 0.421623 Internal.TSS
No -14 0.3 0.00103423 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No -101 -0.39 0.770839 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0143
e.value: 
0.0048
Motif Bicluster: 
e.value: 
130
Motif Bicluster: 
0.53
bicluster_0391
e.value: 
0.00000000000037
Motif Bicluster: 
e.value: 
0.0000039
Motif Bicluster: 
0.53
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
56 - - - - - - -
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
15607223 NP_214595.1 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 GSM1426400 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426401 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426402 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426403 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426404 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426405 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426400 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426401 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426402 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426403 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0081_B125 UCSC Browser Tracks
Rv0081_B236 UCSC Browser Tracks
Rv0081_B288 UCSC Browser Tracks
Rv0081_B451 UCSC Browser Tracks
Rv0081_B452 UCSC Browser Tracks
Rv0081_B453 UCSC Browser Tracks
Rv0081_B454 UCSC Browser Tracks
Rv0081_B542 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.180000 1.05

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: 0.0000000324608
p-value INH: 0.00139529
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 10.64 U
D3I 3 3 3.83 9.89 I
D3U 3 3 3.83 9.37 U
D5I 9 5 6.00 8.58 I
D5U 17 5 6.00 10.80 U
D7I 18 7 8.14 6.92 I
D7U 19 7 8.14 10.06 U
D14I 4 14 15.63 3.26 I
D14U 4 14 15.63 8.26 U
D17I 3 17 19.15 3.92 I
D17U 3 17 19.15 8.44 U
D21I 4 21 23.23 3.88 I
D21U 4 21 23.23 7.77 U
D24I 3 24 26.60 3.58 I
D24U 3 24 26.60 8.02 U
D28I 4 28 30.61 3.78 I
D28U 4 28 30.61 7.39 U