Rv0043c Transcriptional regulator, GntR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0043c Transcriptional regulator, GntR family CDS 47366 48100 - 735 244 TRUE

Rv0043c (Transcriptional regulator, GntR family) is predicted to be co-regulated in modules bicluster_0153 with residual 0.56 and bicluster_0430 with residual 0.49.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.01 and 20.00 for bicluster_0153 and 2,000.00 and 5,600.00 for bicluster_0430 respectively.

These modules are enriched for following go terms: nucleotide metabolic process primary metabolic process, cellular metabolic process, cellular process, organic substance metabolic process.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 2 of 2
Gene Target Differential Expression Distance Expression pvalue Type
L-proline glycine betaine binding ABC transporter protein ProX (TC 3.A.1.12.1)
No 60 -0.55 0.00536884 Primary.TSS
Cell division protein DivIC (FtsB), stabilizes FtsL against RasP cleavage
No -54 0.09 0.95309 Primary.TSS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
transcriptional regulator, ArsR family
No -17 0.1 0.578812 CDS
HTH-type transcriptional regulator
No -2 -0.25 0.380591 CDS
Product (LegacyBRC) Product (RefSeq)
Uncharacterized HTH-type transcriptional regulator Rv0043c_MT0049 GntR family transcriptional regulator
Operon # Operon
28
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
15607185 NP_214557.1 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 GSM1426384 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426385 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426386 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0043c_B215 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.250000 0.56

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: 0.000000000214656
p-value INH: 0.294781
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.01 U
D3I 3 3 3.83 11.81 I
D3U 3 3 3.83 11.61 U
D5I 9 5 6.00 7.94 I
D5U 17 5 6.00 10.75 U
D7I 18 7 8.14 8.38 I
D7U 19 7 8.14 11.87 U
D14I 4 14 15.63 2.41 I
D14U 4 14 15.63 10.28 U
D17I 3 17 19.15 2.31 I
D17U 3 17 19.15 10.66 U
D21I 4 21 23.23 1.11 I
D21U 4 21 23.23 8.97 U
D24I 3 24 26.60 I
D24U 3 24 26.60 10.48 U
D28I 4 28 30.61 I
D28U 4 28 30.61 8.84 U