Rv0465c \Transcriptional regulator, XRE family\\\""

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0465c \Transcriptional regulator, XRE family\\\"" CDS 554882 556306 - 1 425 474 TRUE

Rv0465c (\Transcriptional regulator, XRE family\\\"") is predicted to be co-regulated in modules bicluster_0101 with residual 0.62 and bicluster_0302 with residual 0.49.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.03 for bicluster_0101 and 0.00 and 0.00 for bicluster_0302 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 - 12:11
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15140 MT0481 1684
Displaying 1 - 10 of 42
Gene Target Differential Expression Distance Expression pvalue Type
Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
No 4 -0.26 0.514101 Primary.TSS
Programmed cell death toxin YdcE
No -36 -0.47 0.171524 Primary.TSS
No results were found NA -36 Internal.TSS
Repressed 52 -0.6 0.0000037 Primary.TSS
\Transcriptional regulator, TetR family\\\""
No -27 -0.49 0.00775649 Primary.TSS
Possible membrane protein
No -142 -0.22 0.23185 Primary.TSS
Phosphate transport system permease protein PstC (TC 3.A.1.7.1)
Repressed -131 -1.47 0.000000000000014 CDS
No -112 -0.05 0.914429 Primary.TSS
Transcriptional regulator, XRE family
No 29 -0.11 0.84866 CDS
2-methylcitrate dehydratase (EC 4.2.1.79)
No 8 -0.15 0.841833 CDS
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
311 -
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
15607606 NP_214979.1 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 GSM1426483 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426484 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426485 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426486 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426487 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0465c_B343 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.840000 13.25

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: 0.145348
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.76 U
D3I 3 3 3.83 11.55 I
D3U 3 3 3.83 10.81 U
D5I 9 5 6.00 13.18 I
D5U 17 5 6.00 12.78 U
D7I 18 7 8.14 12.44 I
D7U 19 7 8.14 11.95 U
D14I 4 14 15.63 9.78 I
D14U 4 14 15.63 10.61 U
D17I 3 17 19.15 9.10 I
D17U 3 17 19.15 10.20 U
D21I 4 21 23.23 9.01 I
D21U 4 21 23.23 10.51 U
D24I 3 24 26.60 7.96 I
D24U 3 24 26.60 10.31 U
D28I 4 28 30.61 7.70 I
D28U 4 28 30.61 10.56 U