Rv1719 Transcriptional regulator, IclR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv1719 Transcriptional regulator, IclR family CDS 1945641 1946420 + 780 259 TRUE

Rv1719 (Transcriptional regulator, IclR family) is predicted to be co-regulated in modules bicluster_0221 with residual 0.50 and bicluster_0535 with residual 0.57.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 15.00 and 780.00 for bicluster_0221 and 11.00 and 3,000.00 for bicluster_0535 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 37
Gene Target Differential Expression Distance Expression pvalue Type
Formate hydrogenlyase subunit 4
No 7 0.04 0.963251 CDS
MCE-family lipoprotein LprK (MCE-family lipoprotein Mce1e)
No -50 0.38 0.545137 Internal.TSS
MCE-family protein Mce1F
No -50 0.29 0.557418 Primary.TSS
Metallopeptidase
No -34 0.1 0.812763 Primary.TSS
PPE family protein
No -90 0.47 0.755805 Primary.TSS
ESX-3 secretion system protein EccD3
No -41 -0.16 0.721391 CDS
Peptide deformylase (EC 3.5.1.88)
Repressed 2 -1.39 0.00000536 Primary.TSS
3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Induced -89 0.77 0.0193686 CDS
Diaminopimelate decarboxylase (EC 4.1.1.20)
No 64 0.13 0.741733 CDS
L-aspartate oxidase (EC 1.4.3.16)
No 33 -0.09 0.806159 CDS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, PadR family
No -104 -0.14 0.962221 CDS
Motif 1 Motif 2 Residual
bicluster_0221
e.value: 
15
Motif Bicluster: 
e.value: 
780
Motif Bicluster: 
0.50
bicluster_0535
e.value: 
11
Motif Bicluster: 
e.value: 
3000
Motif Bicluster: 
0.57
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
1115 -
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
15608857 NP_216235.1 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 GSM1426711 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426712 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426713 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1719_B458 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.240000 0.04

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: 0.155584
p-value INH: 0.0414575
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.97 U
D3I 3 3 3.83 15.20 I
D3U 3 3 3.83 15.11 U
D5I 9 5 6.00 13.05 I
D5U 17 5 6.00 13.15 U
D7I 18 7 8.14 14.40 I
D7U 19 7 8.14 14.60 U
D14I 4 14 15.63 14.78 I
D14U 4 14 15.63 15.14 U
D17I 3 17 19.15 14.18 I
D17U 3 17 19.15 15.08 U
D21I 4 21 23.23 13.69 I
D21U 4 21 23.23 14.67 U
D24I 3 24 26.60 12.97 I
D24U 3 24 26.60 14.64 U
D28I 4 28 30.61 12.41 I
D28U 4 28 30.61 14.30 U