Rv0023 Transcriptional regulatory protein

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0023 Transcriptional regulatory protein CDS 27595 28365 + 771 256 TRUE

Rv0023 (Transcriptional regulatory protein) is predicted to be co-regulated in modules bicluster_0304 with residual 0.58 and bicluster_0544 with residual 0.41.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.36 and 78.00 for bicluster_0304 and 420.00 and 780.00 for bicluster_0544 respectively.

These modules are enriched for following go terms: cellular ketone metabolic process cellular homeostasis, homeostatic process, regulation of biological quality, electron carrier activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 174
Gene Target Differential Expression Distance Expression pvalue Type
DNA polymerase III beta subunit (EC 2.7.7.7)
Induced -132 0.63 0.000700791 Primary.TSS
DNA gyrase subunit A (EC 5.99.1.3)
Repressed -58 -1.07 1.81e-19 Internal.TSS
Induced -140 1.04 0.000000121 Internal.TSS
Induced -80 1.04 0.000000121 Internal.TSS
Oxidoreductase
No -25 0.02 0.966411 Internal.TSS
D,D-heptose 7-phosphate kinase
Repressed 32 -1.26 0.000000941 Antisense.TSS
Aldehyde dehydrogenase (EC 1.2.1.3)
No -64 0.25 0.0727037 Primary.TSS
Repressed -69 -0.96 0.0000134 Primary.TSS
MCE-family lipoprotein LprK (MCE-family lipoprotein Mce1e)
Repressed 42 -1.91 1.02e-16 Internal.TSS
MCE-family protein Mce1F
Repressed 42 -1.12 0.00000000033 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
DNA-binding response regulator TrcR
No -97 0.47 0.350351 CDS
Product (LegacyBRC) Product (RefSeq)
Uncharacterized HTH-type transcriptional regulator Rv0023_MT0026 transcriptional regulatory protein
Operon # Operon
15 - -
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
15607165 NP_214537.1 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 GSM1426374 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426375 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426376 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0023_B390 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: 0.000000000260441
p-value INH: 0.0000696472
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D14I 4 14 15.63 6.26 I
D17I 3 17 19.15 5.13 I
D21I 4 21 23.23 5.32 I
D24I 3 24 26.60 4.70 I
D28I 4 28 30.61 5.55 I
D3I 3 3 3.83 11.63 I
D5I 9 5 6.00 12.32 I
D7I 18 7 8.14 8.45 I
D7U 19 7 8.14 11.60 U
D14U 4 14 15.63 9.95 U
D17U 3 17 19.15 9.94 U
D21U 4 21 23.23 9.06 U
D24U 3 24 26.60 9.32 U
D28U 4 28 30.61 8.40 U
D0U 27 0 0.00 12.35 U
D3U 3 3 3.83 11.40 U
D5U 17 5 6.00 12.61 U