Rv2250c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2250c Transcriptional regulator, TetR family CDS 2524785 2525354 - 570 189 TRUE

Rv2250c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0107 with residual 0.57 and bicluster_0461 with residual 0.55.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 3.30 and 320.00 for bicluster_0107 and 23.00 and 620.00 for bicluster_0461 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 152
Gene Target Differential Expression Distance Expression pvalue Type
No -41 -0.55 0.0116904 Primary.TSS
Oxidoreductase
Repressed -131 -0.59 0.0139747 CDS
Lead, cadmium, zinc and mercury transporting ATPase (EC 3.6.3.3) (EC 3.6.3.5); Copper-translocating P-type ATPase (EC 3.6.3.4)
No -50 -0.28 0.413898 Internal.TSS
Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]
No -127 0.14 0.531695 Internal.TSS
Peptide methionine sulfoxide reductase MsrA (EC 1.8.4.11)
Repressed 10 -2.92 8.87e-29 Primary.TSS
Repressed -13 -3.62 5.60519e-45 Primary.TSS
No -50 0.12 0.789662 Primary.TSS
Possible lipoprotein LprO
No 65 -0.29 0.229636 Primary.TSS
Transcriptional regulator, TetR family
Repressed -59 -1.61 0.00103123 CDS
Possible membrane protein
Repressed -21 -1.26 2.88e-20 Primary.TSS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No -133 0.46 0.497969 CDS
Transcriptional regulator, TetR family
Induced -4 5.65 0 CDS
Transcriptional regulator, TetR family
No 4 -0.34 0.642563 CDS
Motif 1 Motif 2 Residual
bicluster_0107
e.value: 
3.3
Motif Bicluster: 
e.value: 
320
Motif Bicluster: 
0.57
bicluster_0461
e.value: 
23
Motif Bicluster: 
e.value: 
620
Motif Bicluster: 
0.55
Product (LegacyBRC) Product (RefSeq)
Uncharacterized HTH-type transcriptional regulator Rv2250c_MT2310 transcriptional regulator
Operon # Operon
1478 -
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
57116959 NP_216766.2 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 GSM1426805 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426806 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426807 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2250c_B617 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.670000 1.02

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: 0.00000000116633
p-value INH: 0.910292
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 10.01 U
D3I 3 3 3.83 9.38 I
D3U 3 3 3.83 9.58 U
D5I 9 5 6.00 11.08 I
D5U 17 5 6.00 12.64 U
D7I 18 7 8.14 7.09 I
D7U 19 7 8.14 9.43 U
D14I 4 14 15.63 4.67 I
D14U 4 14 15.63 6.80 U
D17I 3 17 19.15 I
D17U 3 17 19.15 5.89 U
D21I 4 21 23.23 2.16 I
D21U 4 21 23.23 5.60 U
D24I 3 24 26.60 I
D24U 3 24 26.60 5.14 U
D28I 4 28 30.61 I
D28U 4 28 30.61 5.35 U