Rv3260c Sporulation regulatory protein WhiB

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3260c whiB2 Sporulation regulatory protein WhiB CDS 3639872 3640141 - 270 89 TRUE

Rv3260c (Sporulation regulatory protein WhiB) is predicted to be co-regulated in modules bicluster_0206 with residual 0.59 and bicluster_0316 with residual 0.52.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 400.00 and 10,000.00 for bicluster_0206 and 0.49 and 70.00 for bicluster_0316 respectively.

These modules are enriched for following go terms: nucleotide biosynthetic process, nucleoside phosphate biosynthetic proces..., nucleotide metabolic process, hydroxymethyl-, formyl- and related tran....

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-1.619 -34 3640209 3640243 3640141
Displaying 1 - 10 of 15
Gene Target Differential Expression Distance Expression pvalue Type
Putative phiRv1 phage protein
Induced 25 0.84 0.0154878 Primary.TSS
Undecaprenyl-diphosphatase (EC 3.6.1.27)
No 33 0.22 0.315432 Primary.TSS
No 33 0.37 0.255853 Internal.TSS
No -2 0.37 0.255853 Antisense.TSS
No -72 0.37 0.255853 CDS
Lipoprotein LppL
No -2 0.23 0.31329 Primary.TSS
Induced -16 0.85 0.000102061 Primary.TSS
No -16 0.56 0.0177084 Internal.TSS
Induced -2 1.17 0.000846626 CDS
Induced -23 1.17 0.000846626 Internal.TSS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
DNA-binding response regulator TrcR
No 54 -0.08 0.953506 Primary.TSS
transcriptional regulator, ArsR family
Repressed 67 -1.23 0.000000000272 Primary.TSS
Transcriptional regulator, TetR family
No -3 -0.05 0.952123 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0206
e.value: 
400
Motif Bicluster: 
e.value: 
10000
Motif Bicluster: 
0.59
bicluster_0316
e.value: 
0.49
Motif Bicluster: 
e.value: 
70
Motif Bicluster: 
0.52
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB2 transcriptional regulatory protein WHIB-like WHIB2
Operon # Operon
2134
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
15610396 NP_217777.1 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 GSM1426965 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426966 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426967 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3260c_B335 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: 0.0000000391865
p-value INH: 0.0000744403
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.22 U
D3I 3 3 3.83 14.26 I
D3U 3 3 3.83 13.89 U
D5I 9 5 6.00 9.76 I
D5U 17 5 6.00 12.03 U
D7I 18 7 8.14 10.60 I
D7U 19 7 8.14 14.21 U
D14I 4 14 15.63 6.37 I
D14U 4 14 15.63 13.44 U
D17I 3 17 19.15 3.61 I
D17U 3 17 19.15 13.55 U
D21I 4 21 23.23 3.44 I
D21U 4 21 23.23 13.14 U
D24I 3 24 26.60 2.33 I
D24U 3 24 26.60 13.12 U
D28I 4 28 30.61 3.27 I
D28U 4 28 30.61 12.73 U