Rv3066 Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3066 Transcriptional regulator, TetR family CDS 3430707 3431315 + 609 202 TRUE

Rv3066 (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0385 with residual 0.48 and bicluster_0534 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.63 and 9.20 for bicluster_0385 and 0.00 and 0.02 for bicluster_0534 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 14
Gene Target Differential Expression Distance Expression pvalue Type
Conserved alanine and proline rich protein
No -29 -0.16 0.821224 Primary.TSS
probable conserved membrane protein
No -131 0.08 0.842144 CDS
No 12 0.13 0.884822 Internal.TSS
No 55 -0.31 0.520297 CDS
Protein export cytoplasm protein SecA ATPase RNA helicase (TC 3.A.5.1.1)
No -79 0.18 0.179684 Internal.TSS
Protein export cytoplasm protein SecA ATPase RNA helicase (TC 3.A.5.1.1)
No 11 0.18 0.179684 CDS
Multidrug resistance protein mmr
Repressed 1 -2.28 1.44e-22 Primary.TSS
Molybdenum cofactor biosynthesis protein MoaC
No -131 -0.15 0.80714 CDS
No 67 -0.33 0.314974 Primary.TSS
Probable response regulator
No -41 -0.6 0.344505 CDS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, IclR family
No -10 -0.16 0.88719 Internal.TSS
Motif 1 Motif 2 Residual
bicluster_0385
e.value: 
0.63
Motif Bicluster: 
e.value: 
9.2
Motif Bicluster: 
0.48
bicluster_0534
e.value: 
0.0000000021
Motif Bicluster: 
e.value: 
0.017
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY DEOR-FAMILY] DeoR family transcriptional regulator
Operon # Operon
2009 -
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
15610203 NP_217582.1 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 GSM1426907 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426908 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426909 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426910 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426911 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426912 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3066_B153 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.150000 0.28

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: 0.107395
p-value INH: 0.776531
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 10.29 U
D3I 3 3 3.83 9.56 I
D3U 3 3 3.83 9.04 U
D5I 9 5 6.00 12.12 I
D5U 17 5 6.00 11.66 U
D7I 18 7 8.14 10.87 I
D7U 19 7 8.14 9.87 U
D14I 4 14 15.63 9.26 I
D14U 4 14 15.63 8.25 U
D17I 3 17 19.15 9.34 I
D17U 3 17 19.15 7.87 U
D21I 4 21 23.23 9.85 I
D21U 4 21 23.23 7.83 U
D24I 3 24 26.60 10.36 I
D24U 3 24 26.60 7.46 U
D28I 4 28 30.61 9.99 I
D28U 4 28 30.61 8.00 U