Rv0474 \Transcriptional regulator, XRE family\\\""

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0474 \Transcriptional regulator, XRE family\\\"" CDS 565021 565443 + 423 140 TRUE

Rv0474 (\Transcriptional regulator, XRE family\\\"") is predicted to be co-regulated in modules bicluster_0167 with residual 0.51 and bicluster_0593 with residual 0.58.

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 4,900.00 and 7,400.00 for bicluster_0593 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 9 of 9
Gene Target Differential Expression Distance Expression pvalue Type
Iron-regulated heparin binding hemagglutinin HbhA (Adhesin)
No -32 -0.49 0.00980992 CDS
DNA-directed RNA polymerase beta subunit (EC 2.7.7.6)
No 23 -0.04 0.929016 Primary.TSS
Induced -79 0.77 0.0415257 Primary.TSS
No -72 0.1 0.858135 CDS
No -90 -0.26 0.689564 Primary.TSS
PE family protein
No -6 0.08 0.957749 Primary.TSS
FIG055075: Possibly a cell division protein, antigen 84 in Mycobacteria
No 60 0.02 0.957474 Primary.TSS
Translation initiation factor 1
No -67 -0.2 0.743863 Primary.TSS
Histone protein Lsr2
No 33 -0.02 0.978361 Primary.TSS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
Induced -63 0.67 0.0156278 Primary.TSS
HTH-type transcriptional regulator
No -66 0.05 0.900162 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0167
e.value: 
0.0021
Motif Bicluster: 
e.value: 
49
Motif Bicluster: 
0.51
bicluster_0593
e.value: 
4900
Motif Bicluster: 
e.value: 
7400
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
320
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
15607615 NP_214988.1 Run
GO:0005829

cytosol

cytosol

Details: 
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO Category: 
cellular_component
371
Total items in this category:  
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 GSM1426491 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426492 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426493 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426494 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0474_B122 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.510000 0.52

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: 0.00000586319
p-value INH: 0.852778
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.34 U
D3I 3 3 3.83 12.85 I
D3U 3 3 3.83 12.31 U
D5I 9 5 6.00 12.36 I
D5U 17 5 6.00 12.06 U
D7I 18 7 8.14 13.13 I
D7U 19 7 8.14 12.06 U
D14I 4 14 15.63 12.39 I
D14U 4 14 15.63 11.16 U
D17I 3 17 19.15 11.99 I
D17U 3 17 19.15 10.47 U
D21I 4 21 23.23 12.22 I
D21U 4 21 23.23 10.82 U
D24I 3 24 26.60 11.99 I
D24U 3 24 26.60 10.31 U
D28I 4 28 30.61 12.18 I
D28U 4 28 30.61 10.54 U