Rv0020c

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0020c fhaA CDS 23861 25444 - 1 584 527 TRUE

Rv0020c () is predicted to be co-regulated in modules bicluster_0026 with residual 0.58 and bicluster_0365 with residual 0.53.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.18 and 1.60 for bicluster_0026 and 0.00 and 8,900.00 for bicluster_0365 respectively.

These modules are enriched for following go terms: .

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

Mutant available?: Yes

Last update: 10/16/2017 - 16:54
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15122 MT0023 1025
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
DNA-binding response regulator TrcR
No -45 -0.4 0.000800963 Primary.TSS
Transcriptional regulator, ArsR family
No -58 -0.12 0.380643 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0026
e.value: 
0.18
Motif Bicluster: 
e.value: 
1.6
Motif Bicluster: 
0.58
bicluster_0365
e.value: 
0.0049
Motif Bicluster: 
e.value: 
8900
Motif Bicluster: 
0.53
Product (LegacyBRC) Product (RefSeq)
Putative uncharacterized protein TB398
Operon # Operon
12 Rv0020c
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
15607162 NP_214534.1 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 GSM1426368 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426369 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426370 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0020c_B385 UCSC Browser Tracks
Quantitative Proteomics Data
Cholesterol Essentiality t-test p-value Cholesterol/Glycerol Ratio
non-essential 0.670000 1.18

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 11.95 U
D3I 3 3 3.83 12.39 I
D3U 3 3 3.83 12.08 U
D5I 9 5 6.00 12.71 I
D5U 17 5 6.00 12.65 U
D7I 18 7 8.14 13.01 I
D7U 19 7 8.14 12.36 U
D14I 4 14 15.63 11.59 I
D14U 4 14 15.63 11.84 U
D17I 3 17 19.15 12.15 I
D17U 3 17 19.15 12.41 U
D21I 4 21 23.23 11.22 I
D21U 4 21 23.23 12.16 U
D24I 3 24 26.60 11.88 I
D24U 3 24 26.60 13.00 U
D28I 4 28 30.61 10.69 I
D28U 4 28 30.61 12.61 U