Rv2034 Transcriptional regulator, ArsR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2034 Transcriptional regulator, ArsR family CDS 2281294 2281617 + 324 107 TRUE

Rv2034 (Transcriptional regulator, ArsR family) is predicted to be co-regulated in modules bicluster_0120 with residual 0.55 and bicluster_0546 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 0.00 for bicluster_0120 and 0.00 and 0.21 for bicluster_0546 respectively.

These modules are enriched for following go terms: nucleic acid binding transcription facto..., sequence-specific DNA binding transcript... .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 150
Gene Target Differential Expression Distance Expression pvalue Type
Chromosomal replication initiator protein DnaA
No -80 -0.56 0.00145696 Primary.TSS
No 30 -0.5 0.00880736 Primary.TSS
Oxidoreductase
No 19 -0.1 0.864515 CDS
Transcriptional regulator, TetR family
No -43 -0.55 0.165464 CDS
LSU ribosomal protein L28p
No -90 0 0.99953 CDS
Transmembrane acyltransferase (EC:2.3.1.-)
No 63 0.1 0.767878 Primary.TSS
GDP-mannose 4,6 dehydratase (EC 4.2.1.47)
No -84 -0.01 0.989871 Primary.TSS
Histone acetyltransferase HPA2 and related acetyltransferases
No -9 -0.46 0.00000871 Primary.TSS
No -142 -0.12 0.74233 Primary.TSS
NAD(P) transhydrogenase alpha subunit (EC 1.6.1.2)
No -94 -0.17 0.544837 CDS
Displaying 1 - 6 of 6
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No 33 -0.18 0.912567 CDS
Transcriptional regulator, ArsR family
Repressed -22 -2.91 0.000000000000197 CDS
Transcriptional regulatory protein
Induced -27 2.78 0.000000000000317 CDS
transcriptional regulator, ArsR family
Induced -20 1.48 0.0000000651 CDS
Transcriptional regulator, ArsR family
Induced -11 3.86 1.13e-35 CDS
Two component transcriptional regulatory protein DevR
No -54 -0.04 0.918782 CDS
Motif 1 Motif 2 Residual
bicluster_0120
e.value: 
0.0000000099
Motif Bicluster: 
e.value: 
0.0001
Motif Bicluster: 
0.55
bicluster_0546
e.value: 
0.0017
Motif Bicluster: 
e.value: 
0.21
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
Probable ArsR-type repressor protein ArsR-type repressor protein
Operon # Operon
1335 - -
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
15609171 NP_216550.1 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 GSM1426785 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426786 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426787 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426788 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426789 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426785 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426786 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426787 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426788 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426789 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2034_B141 UCSC Browser Tracks
Rv2034_B151 UCSC Browser Tracks
Rv2034_B171 UCSC Browser Tracks
Rv2034_B225 UCSC Browser Tracks
Rv2034_B545 UCSC Browser Tracks
Rv2034_B560 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.150000 0.06

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: 0.000000918846
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 10.48 U
D3I 3 3 3.83 10.74 I
D3U 3 3 3.83 10.88 U
D5I 9 5 6.00 8.69 I
D5U 17 5 6.00 10.11 U
D7I 18 7 8.14 6.93 I
D7U 19 7 8.14 9.41 U
D14I 4 14 15.63 2.80 I
D14U 4 14 15.63 9.76 U
D17I 3 17 19.15 I
D17U 3 17 19.15 9.50 U
D21I 4 21 23.23 2.16 I
D21U 4 21 23.23 9.28 U
D24I 3 24 26.60 I
D24U 3 24 26.60 9.11 U
D28I 4 28 30.61 I
D28U 4 28 30.61 8.90 U