Rv3124 transcriptional regulator, AfsR/DnrI/RedD family

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3124 moaR1 transcriptional regulator, AfsR/DnrI/RedD family CDS 3489506 3490375 + 870 289 TRUE

Rv3124 (transcriptional regulator, AfsR/DnrI/RedD family) is predicted to be co-regulated in modules bicluster_0091 with residual 0.52 and bicluster_0092 with residual 0.47.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 12.00 for bicluster_0091 and 490.00 and 6,500.00 for bicluster_0092 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score Distance to Tuberculist Start Codon Internal TSS Re-Annotated Start Tuberculist Annotated Start
-0.523 666 3490172 3489482 3489506
Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-18382 MT3208 2144
Displaying 1 - 2 of 2
Gene Target Differential Expression Distance Expression pvalue Type
No -118 0.37 0.953654 Primary.TSS
Type VII secretion integral membrane protein EccD
No -73 0.04 0.956095 Primary.TSS
Displaying 1 - 6 of 6
ChipSeq TF Differential Expression Distance Expression pvalue Type
Histone protein Lsr2
No 28 0.07 0.897742 CDS
Transcriptional regulator, TetR family
No -47 0.16 0.756541 Internal.TSS
RNA polymerase sigma-54 factor RpoN
No -126 -0.11 0.994822 Internal.TSS
Transcriptional regulatory protein
No -88 0.22 0.39331 Internal.TSS
Transcriptional regulator, PadR family
No -20 0.48 0.182279 Internal.TSS
transcriptional regulator, ArsR family
Induced 11 0.91 0.0000000108 CDS
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
2040
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
15610261 NP_217640.1 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 GSM1426921 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426922 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426923 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3124_B227 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.070000 0.58

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: 0.00834979
p-value INH: 0.439162
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.96 U
D3I 3 3 3.83 13.63 I
D3U 3 3 3.83 13.29 U
D5I 9 5 6.00 13.66 I
D5U 17 5 6.00 13.52 U
D7I 18 7 8.14 14.10 I
D7U 19 7 8.14 13.75 U
D14I 4 14 15.63 12.99 I
D14U 4 14 15.63 13.22 U
D17I 3 17 19.15 13.26 I
D17U 3 17 19.15 13.43 U
D21I 4 21 23.23 12.97 I
D21U 4 21 23.23 13.38 U
D24I 3 24 26.60 12.50 I
D24U 3 24 26.60 13.33 U
D28I 4 28 30.61 12.28 I
D28U 4 28 30.61 13.11 U