Rv2595

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv2595 vapB40 CDS 2925492 2925737 + 246 81 TRUE

Rv2595 () is predicted to be co-regulated in modules bicluster_0138 with residual 0.67 and bicluster_0304 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.42 for bicluster_0138 and 0.36 and 78.00 for bicluster_0304 respectively.

These modules are enriched for following go terms: cellular ketone metabolic process.

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
Induced 50 1.69 0.00000126 Primary.TSS
Displaying 1 - 4 of 4
ChipSeq TF Differential Expression Distance Expression pvalue Type
Induced 50 1.69 0.00000126 Primary.TSS
transcriptional regulator, ArsR family
Induced -36 0.6 0.0127074 Primary.TSS
Transcriptional regulator, AraC family
No -129 -0.16 0.960731 Primary.TSS
No -42 0.11 0.874323 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
Uncharacterized protein Rv2595_MT26711
Operon # Operon
1704 -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics
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
15609732 NP_217111.1 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 GSM1426835 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426836 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426837 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2595_B375 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
NA NA

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: 0.00165718
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.11 U
D3I 3 3 3.83 13.22 I
D3U 3 3 3.83 13.00 U
D5I 9 5 6.00 13.98 I
D5U 17 5 6.00 13.57 U
D7I 18 7 8.14 13.95 I
D7U 19 7 8.14 13.09 U
D14I 4 14 15.63 12.89 I
D14U 4 14 15.63 11.75 U
D17I 3 17 19.15 12.69 I
D17U 3 17 19.15 11.15 U
D21I 4 21 23.23 13.14 I
D21U 4 21 23.23 11.65 U
D24I 3 24 26.60 12.78 I
D24U 3 24 26.60 11.04 U
D28I 4 28 30.61 13.17 I
D28U 4 28 30.61 11.42 U