Rv2021c Transcriptional regulator, XRE family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2021c Transcriptional regulator, XRE family CDS 2266805 2267110 - 306 101 TRUE

Rv2021c (Transcriptional regulator, XRE family) is predicted to be co-regulated in modules bicluster_0238 with residual 0.51 and bicluster_0505 with residual 0.54.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 1,400.00 and 8,600.00 for bicluster_0238 and 0.00 and 0.00 for bicluster_0505 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 25
Gene Target Differential Expression Distance Expression pvalue Type
Possible membrane protein
No -24 0.04 0.921925 Internal.TSS
Antigen 85-C precursor (85C) (Antigen 85 complex C) (Ag85C) (Mycolyl transferase 85C) (EC 2.3.1.-)
No -33 0.02 0.979426 Primary.TSS
CTP:molybdopterin cytidylyltransferase
No -25 0.02 0.973087 Primary.TSS
PPE family protein
No -2 0.12 0.887052 CDS
probable RNA methyltransferase
No -107 0.17 0.754282 CDS
Anti-sigma F factor antagonist (spoIIAA-2); Anti-sigma B factor antagonist RsbV
No -115 -0.24 0.773639 Primary.TSS
No -86 0.04 0.975545 CDS
Carboxylesterase, type B
No 66 0.25 0.0995656 Antisense.TSS
Carboxylesterase, type B
No 69 0.25 0.0995656 CDS
HAD-superfamily subfamily IIA hydrolase, hypothetical 2
No -43 -0.09 0.836542 CDS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No results were found
Motif 1 Motif 2 Residual
bicluster_0238
e.value: 
1400
Motif Bicluster: 
e.value: 
8600
Motif Bicluster: 
0.51
bicluster_0505
e.value: 
0.000016
Motif Bicluster: 
e.value: 
0.00038
Motif Bicluster: 
0.54
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
1327 - -
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
15609158 NP_216537.1 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 GSM1426780 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426781 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426782 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426783 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426784 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2021c_B140 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.900000 0.45

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: 0.00046196
p-value INH: 0.852778
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.51 U
D3I 3 3 3.83 13.72 I
D3U 3 3 3.83 13.72 U
D5I 9 5 6.00 13.83 I
D5U 17 5 6.00 13.54 U
D7I 18 7 8.14 14.12 I
D7U 19 7 8.14 13.34 U
D14I 4 14 15.63 12.66 I
D14U 4 14 15.63 12.16 U
D17I 3 17 19.15 11.62 I
D17U 3 17 19.15 11.47 U
D21I 4 21 23.23 12.09 I
D21U 4 21 23.23 12.05 U
D24I 3 24 26.60 11.14 I
D24U 3 24 26.60 11.32 U
D28I 4 28 30.61 11.75 I
D28U 4 28 30.61 11.76 U