Rv0067c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0067c Transcriptional regulator, TetR family CDS 74629 75198 - 570 189 TRUE

Rv0067c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0018 with residual 0.62 and bicluster_0527 with residual 0.54.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.55 and 25.00 for bicluster_0018 and 0.47 and 120.00 for bicluster_0527 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 3 of 3
Gene Target Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
Induced 43 4.05 0 CDS
Oxidoreductase/Short-chain dehydrogenase
Repressed -14 -1.3 0.000485517 Primary.TSS
PE family protein
No 7 -0.65 0.876941 Primary.TSS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
Induced 43 4.05 0 CDS
Transcriptional regulator, MarR family
No -98 -0.39 0.306631 CDS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [POSSIBLY TETR-FAMILY] TetR family transcriptional regulator
Operon # Operon
45
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
15607209 NP_214581.1 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 GSM1426393 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426394 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426395 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0067c_B392 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.570000 2.36

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: 0.31313
p-value INH: 0.895957
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 5.37 U
D3I 3 3 3.83 3.33 I
D3U 3 3 3.83 3.64 U
D5I 9 5 6.00 I
D5U 17 5 6.00 U
D7I 18 7 8.14 6.10 I
D7U 19 7 8.14 5.81 U
D14I 4 14 15.63 3.35 I
D14U 4 14 15.63 2.34 U
D17I 3 17 19.15 4.49 I
D17U 3 17 19.15 3.37 U
D21I 4 21 23.23 3.75 I
D21U 4 21 23.23 2.37 U
D24I 3 24 26.60 3.58 I
D24U 3 24 26.60 2.57 U
D28I 4 28 30.61 3.55 I
D28U 4 28 30.61 3.05 U