Rv2011c Transcriptional regulator, MarR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2011c Transcriptional regulator, MarR family CDS 2258854 2259285 - 432 143 TRUE

Rv2011c (Transcriptional regulator, MarR family) is predicted to be co-regulated in modules bicluster_0291 with residual 0.49 and bicluster_0346 with residual 0.51.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 3.30 for bicluster_0291 and 0.00 and 0.14 for bicluster_0346 respectively.

These modules are enriched for following go terms: acyl-CoA dehydrogenase activity .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 79
Gene Target Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No -98 -0.39 0.306631 CDS
Serine hydroxymethyltransferase (EC 2.1.2.1)
Repressed 64 -1.9 0.0000000000216 Primary.TSS
Retron-type RNA-directed DNA polymerase (EC 2.7.7.49)
No -108 -0.4 0.104664 CDS
Transcriptional regulator, TetR family
Repressed 13 -1.24 0.000249174 Primary.TSS
FIG030769: Probable conserved MCE associated membrane protein
No 11 -0.18 0.210461 Primary.TSS
Alanine transaminase (EC 2.6.1.2)
No -10 -0.26 0.133246 CDS
COG2907: Amine oxidase, flavin-containing
No -75 -0.03 0.946128 CDS
Possible membrane protein
Repressed -108 -0.98 0.00000000112 Primary.TSS
MCE-family protein Mce1F
No -87 -0.41 0.265403 Internal.TSS
Preprotein translocase subunit SecE (TC 3.A.5.1.1)
No -30 -0.22 0.405896 Primary.TSS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, MarR family
Induced 32 4.72 0 CDS
Beta-carotene ketolase (EC 1.14.-.-)
No 37 -0.13 0.999473 CDS
Product (LegacyBRC) Product (RefSeq)
Uncharacterized protein Rv2011c_MT2066
Operon # Operon
1320
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
15609148 NP_216527.1 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 GSM1426774 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426775 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426776 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2011c_B374 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.620000 4.10

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: 0.392434
p-value INH: 0.0524689
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D3I 3 3 3.83 14.66 I
D3U 3 3 3.83 14.70 U
D17I 3 17 19.15 9.92 I
D17U 3 17 19.15 12.91 U
D24I 3 24 26.60 6.46 I
D24U 3 24 26.60 12.29 U
D14I 4 14 15.63 12.53 I
D14U 4 14 15.63 13.70 U
D21I 4 21 23.23 9.25 I
D21U 4 21 23.23 13.12 U
D28I 4 28 30.61 6.92 I
D28U 4 28 30.61 12.27 U
D5I 9 5 6.00 13.66 I
D5U 17 5 6.00 13.47 U
D7I 18 7 8.14 14.54 I
D7U 19 7 8.14 14.34 U
D0U 27 0 0.00 14.56 U