Rv3862c Transcriptional regulator WhiB-like WhiB6

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3862c whiB6 Transcriptional regulator WhiB-like WhiB6 CDS 4338171 4338521 - 351 116 TRUE

Rv3862c (Transcriptional regulator WhiB-like WhiB6) is predicted to be co-regulated in modules bicluster_0224 with residual 0.55 and bicluster_0238 with residual 0.51.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 480.00 and 27.00 for bicluster_0224 and 1,400.00 and 8,600.00 for bicluster_0238 respectively.

These modules are enriched for following go terms: regulation of cellular process, regulation of biological process, biological regulation .

This gene is found to be non-essential for growth on cholesterol.

Mutant available?: Yes

BASS Score Re-Annotated Start Tuberculist Annotated Start
-0.992 4338461 4338521
Last update: 10/16/2017 - 16:54
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15060 MT3976 1286
Displaying 1 - 6 of 6
Gene Target Differential Expression Distance Expression pvalue Type
No -86 0.22 0.726669 Primary.TSS
ESX-1 secretion system protein (Rv3616c)
No -125 0.21 0.620835 Primary.TSS
Cysteine desulfurase (EC 2.8.1.7)
Repressed -3 -0.65 0.0000133 Primary.TSS
Repressed -20 -0.82 0.0000533 Primary.TSS
PE family protein
Induced 61 1.52 0.000000000000422 Primary.TSS
Induced 1 1.24 1.03e-26 CDS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
Organic hydroperoxide resistance transcriptional regulator
Induced -72 1.67 0.0217509 CDS
Transcriptional regulatory protein
No -28 -0.51 0.427657 CDS
transcriptional regulator, ArsR family
Induced -14 2.17 0.0000000189 CDS
Motif 1 Motif 2 Residual
bicluster_0224
e.value: 
480
Motif Bicluster: 
e.value: 
27
Motif Bicluster: 
0.55
bicluster_0238
e.value: 
1400
Motif Bicluster: 
e.value: 
8600
Motif Bicluster: 
0.51
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB6 transcriptional regulatory protein WHIB-like WHIB6
Operon # Operon
2527 Rv3862c
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
15610998 NP_218379.1 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 GSM1427056 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427057 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427058 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427059 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3862c_B170 UCSC Browser Tracks
Quantitative Proteomics Data
Cholesterol Essentiality t-test p-value Cholesterol/Glycerol Ratio
non-essential 0.140000 1.05

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.

Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.44 U
D3I 3 3 3.83 12.08 I
D3U 3 3 3.83 12.38 U
D5I 9 5 6.00 11.32 I
D5U 17 5 6.00 11.67 U
D7I 18 7 8.14 11.66 I
D7U 19 7 8.14 11.81 U
D14I 4 14 15.63 8.69 I
D14U 4 14 15.63 9.84 U
D17I 3 17 19.15 7.02 I
D17U 3 17 19.15 9.04 U
D21I 4 21 23.23 5.85 I
D21U 4 21 23.23 8.71 U
D24I 3 24 26.60 3.97 I
D24U 3 24 26.60 8.14 U
D28I 4 28 30.61 3.57 I
D28U 4 28 30.61 7.65 U