Rv0623

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0623 vapB30 CDS 716410 716664 + 255 84 TRUE

Rv0623 () is predicted to be co-regulated in modules bicluster_0193 with residual 0.55 and bicluster_0537 with residual 0.59.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.04 for bicluster_0193 and 0.00 and 0.04 for bicluster_0537 respectively.

These modules are enriched for following go terms: response to stress, cellular response to stimulus, single-organism cellular process, nucleic acid metabolic process, four-way junction helicase activity, endodeoxyribonuclease activity, hydrolase activity, acting on ester bond....

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 -45 2.39 1.15e-27 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Induced -45 2.39 1.15e-27 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
Putative uncharacterized protein
Operon # Operon
419 -
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
15607763 NP_215137.1 Run
GO:0045927

positive regulation of growth

positive regulation of growth

Details: 
Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism.
GO Category: 
biological_process
31
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 GSM1426521 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426522 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426523 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0623_B364 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:
p-value INH: