Rv1556 Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv1556 Transcriptional regulator, TetR family CDS 1760997 1761605 + 609 202 TRUE

Rv1556 (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0218 with residual 0.55 and bicluster_0578 with residual 0.46.

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_0218 and 920.00 and 1,000.00 for bicluster_0578 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score Distance to Tuberculist Start Codon Internal TSS New Internal UTR Re-Annotated Start Tuberculist Annotated Start
-0.413 12 1761009 69 1761078 1760997
Last update: 11/20/2020 - 12:11
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-17970 MT1607 1032
Displaying 1 - 10 of 13
Gene Target Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No 44 -0.07 0.984804 CDS
Cytochrome P450 138
No -73 0.24 0.98469 CDS
ATP synthase alpha chain (EC 3.6.3.14)
No -61 -0.03 0.990711 CDS
9.5 kDa culture filtrate antigen Cfp10A
No -24 0.05 0.984804 CDS
Transcriptional regulator, TetR family
Induced -22 3.04 4.56e-19 CDS
No -29 0.02 0.999823 CDS
Probable phiRV1 phage protein
No -45 0.35 0.98469 CDS
Transcriptional regulatory protein glnR
No -32 -0.05 0.991185 CDS
Sulfur carrier protein adenylyltransferase ThiF
No 44 -0.04 0.984804 Antisense.TSS
Sulfur carrier protein adenylyltransferase ThiF
No -123 -0.04 0.984804 CDS
Displaying 1 - 4 of 4
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No -29 0.04 0.97077 Internal.TSS
Transcriptional regulator, TetR family
Induced -22 3.04 4.56e-19 CDS
Transcriptional regulator, TetR family
No -89 -0.14 0.843035 Internal.TSS
Transcriptional regulator, TetR family
No -77 -0.14 0.843035 CDS
Product (LegacyBRC) Product (RefSeq)
Uncharacterized HTH-type transcriptional regulator Rv1556_MT1607 regulatory protein
Operon # Operon
1034
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
15608694 NP_216072.1 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 GSM1426693 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426694 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426695 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1556_B445 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.600000 1.78

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: 0.304876
p-value INH: 0.910292
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.59 U
D3I 3 3 3.83 13.05 I
D3U 3 3 3.83 12.72 U
D5I 9 5 6.00 13.16 I
D5U 17 5 6.00 13.04 U
D7I 18 7 8.14 13.63 I
D7U 19 7 8.14 13.27 U
D14I 4 14 15.63 11.34 I
D14U 4 14 15.63 11.67 U
D17I 3 17 19.15 10.70 I
D17U 3 17 19.15 11.31 U
D21I 4 21 23.23 10.62 I
D21U 4 21 23.23 11.65 U
D24I 3 24 26.60 9.73 I
D24U 3 24 26.60 11.18 U
D28I 4 28 30.61 9.73 I
D28U 4 28 30.61 11.28 U