Rv1423

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv1423 whiA CDS 1597906 1598883 + 978 325 TRUE

Rv1423 () is predicted to be co-regulated in modules bicluster_0266 with residual 0.50 and bicluster_0329 with residual 0.54.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 41.00 and 620.00 for bicluster_0266 and 0.00 and 1.10 for bicluster_0329 respectively.

These modules are enriched for following go terms: inositol metabolic process, inositol biosynthetic process, polyol biosynthetic process, acyl-CoA dehydrogenase activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Re-Annotated Start Tuberculist Annotated Start
-0.031 1597900 1597906
Displaying 1 - 10 of 119
Gene Target Differential Expression Distance Expression pvalue Type
No 62 -0.09 0.81591 Primary.TSS
No -42 0.03 0.944781 Internal.TSS
No 11 0.03 0.944781 Internal.TSS
Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Repressed 60 -0.92 0.000000501 Primary.TSS
Cell division protein DivIC (FtsB), stabilizes FtsL against RasP cleavage
No -129 0.47 0.0513214 Internal.TSS
Cell division protein DivIC (FtsB), stabilizes FtsL against RasP cleavage
No -64 0.47 0.0513214 Internal.TSS
Transcriptional regulator, TetR family
No 51 0.54 0.313819 Primary.TSS
PE-PGRS family protein
No 23 -0.03 0.944837 Primary.TSS
Chaperone protein DnaK
No -83 -0.07 0.925331 Primary.TSS
No -149 0.4 0.417884 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No results were found
Motif 1 Motif 2 Residual
bicluster_0266
e.value: 
41
Motif Bicluster: 
e.value: 
620
Motif Bicluster: 
0.50
bicluster_0329
e.value: 
0.00000000023
Motif Bicluster: 
e.value: 
1.1
Motif Bicluster: 
0.54
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIA transcriptional regulatory protein WHIA
Operon # Operon
950 - - -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics
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
15608561 NP_215939.1 Run
GO:0005618

cell wall

cell wall

Details: 
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan.
GO Category: 
cellular_component
320
Total items in this category:  
GO:0005886

plasma membrane

plasma membrane

Details: 
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO Category: 
cellular_component
1284
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 GSM1426676 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426677 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426678 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1423_B442 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
NA NA

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: 0.165664
p-value INH: 0.0145759
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.09 U
D3I 3 3 3.83 13.09 I
D3U 3 3 3.83 12.72 U
D5I 9 5 6.00 10.77 I
D5U 17 5 6.00 10.75 U
D7I 18 7 8.14 12.07 I
D7U 19 7 8.14 12.16 U
D14I 4 14 15.63 4.41 I
D14U 4 14 15.63 8.82 U
D17I 3 17 19.15 2.26 I
D17U 3 17 19.15 8.56 U
D21I 4 21 23.23 1.73 I
D21U 4 21 23.23 7.24 U
D24I 3 24 26.60 1.96 I
D24U 3 24 26.60 7.47 U
D28I 4 28 30.61 I
D28U 4 28 30.61 6.14 U