Rv0330c Transcriptional regulator, TetR family

Summary

Product Feature Type Start End Strand Length AA Length is TF
Rv0330c Transcriptional regulator, TetR family CDS 395347 396087 - 741 246 TRUE

Rv0330c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0167 with residual 0.51 and bicluster_0420 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 49.00 for bicluster_0167 and 0.00 and 0.00 for bicluster_0420 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 11/20/2020 - 12:11
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-14953 MT0345 354
Displaying 1 - 3 of 3
Gene Target Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
Induced 28 5.41 0 CDS
Oxidoreductase (flavoprotein)
No -53 -0.71 0.149297 Primary.TSS
Malonyl CoA-acyl carrier protein transacylase (EC 2.3.1.39)
No 51 0.18 0.948058 CDS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
Induced 28 5.41 0 CDS
Product (LegacyBRC) Product (RefSeq)
Putative uncharacterized protein
Operon # Operon
228 -
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
15607471 NP_214844.1 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 GSM1426461 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426462 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426463 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426464 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426461 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426462 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426463 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426464 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0330c_B349 UCSC Browser Tracks
Rv0330c_B607 UCSC Browser Tracks

Quantitative Proteomics Data

t-test p-value Cholesterol/Glycerol Ratio
0.650000 1.06

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: 0.804636
p-value INH: 0.0414575
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D3I 3 3 3.83 10.38 I
D5I 9 5 6.00 10.61 I
D7I 18 7 8.14 10.43 I
D14I 4 14 15.63 7.76 I
D17I 3 17 19.15 7.32 I
D21I 4 21 23.23 6.26 I
D24I 3 24 26.60 4.99 I
D28I 4 28 30.61 5.05 I
D0U 27 0 0.00 11.48 U
D3U 3 3 3.83 10.16 U
D5U 17 5 6.00 10.53 U
D7U 19 7 8.14 10.21 U
D14U 4 14 15.63 8.10 U
D17U 3 17 19.15 7.34 U
D21U 4 21 23.23 7.60 U
D24U 3 24 26.60 6.52 U
D28U 4 28 30.61 6.62 U