Rv1219c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv1219c Transcriptional regulator, TetR family CDS 1362723 1363361 - 639 212 TRUE

Rv1219c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0078 with residual 0.48 and bicluster_0173 with residual 0.41.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 360.00 and 14,000.00 for bicluster_0078 and 11.00 and 12,000.00 for bicluster_0173 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 28
Gene Target Differential Expression Distance Expression pvalue Type
No 69 0.25 0.448713 Antisense.TSS
TetR/ACRR family transcriptional regulator
No -85 0.53 0.233634 Primary.TSS
ClpB protein
Repressed 13 -1.09 0.000130048 Primary.TSS
Flavohemoprotein (Hemoglobin-like protein) (Flavohemoglobin) (Nitric oxide dioxygenase) (EC 1.14.12.17)
No -98 0.01 0.990105 Primary.TSS
COG4861: Uncharacterized protein conserved in bacteria
No 31 -0.02 0.963712 CDS
Type I antifreeze protein
No -140 0.12 0.905062 Primary.TSS
CONSERVED MEMBRANE PROTEIN
No -20 -0.08 0.831249 CDS
Transcriptional regulator, TetR family
Induced 6 5.07 0 Primary.TSS
Maltose/maltodextrin ABC transporter, permease protein MalG
No -114 -0.15 0.758403 CDS
Possible membrane protein
Repressed -64 -1.03 0.00000000000105 Primary.TSS
Displaying 1 - 4 of 4
ChipSeq TF Differential Expression Distance Expression pvalue Type
No 55 0.44 0.238346 Primary.TSS
Transcriptional regulator, MarR family
No 6 0.54 0.383054 Primary.TSS
Adenylyl cyclase class-3/4/guanylyl cyclase / Disease resistance domain-containing protein / Tetratricopeptide repeat-containing protein / Transcriptional regulator, LuxR family
No -1 -0.22 0.999776 Primary.TSS
Transcriptional regulator, TetR family
Induced 6 5.07 0 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0078
e.value: 
360
Motif Bicluster: 
e.value: 
14000
Motif Bicluster: 
0.48
bicluster_0173
e.value: 
11
Motif Bicluster: 
e.value: 
12000
Motif Bicluster: 
0.41
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
829 - - - -
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
15608359 NP_215735.1 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 GSM1426637 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426638 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426639 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1219c_B487 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.240000 1.27

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: 0.00000000247893
p-value INH: 0.00821252
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.95 U
D3I 3 3 3.83 13.62 I
D3U 3 3 3.83 13.44 U
D5I 9 5 6.00 11.35 I
D5U 17 5 6.00 13.09 U
D7I 18 7 8.14 10.73 I
D7U 19 7 8.14 13.26 U
D14I 4 14 15.63 4.26 I
D14U 4 14 15.63 11.28 U
D17I 3 17 19.15 2.31 I
D17U 3 17 19.15 10.44 U
D21I 4 21 23.23 3.66 I
D21U 4 21 23.23 9.35 U
D24I 3 24 26.60 I
D24U 3 24 26.60 9.53 U
D28I 4 28 30.61 I
D28U 4 28 30.61 8.55 U