Rv3183 FIG036183: Transcriptional regulator, XRE family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3183 FIG036183: Transcriptional regulator, XRE family CDS 3550715 3551044 + 330 109 TRUE

Rv3183 (FIG036183: Transcriptional regulator, XRE family) is predicted to be co-regulated in modules bicluster_0120 with residual 0.55 and bicluster_0180 with residual 0.54.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.00 for bicluster_0120 and 19,000.00 and 20,000.00 for bicluster_0180 respectively.

These modules are enriched for following go terms: nucleic acid binding transcription facto..., sequence-specific DNA binding transcript... cellular macromolecule biosynthetic proc..., macromolecule biosynthetic process, regulation of transcription, DNA-depende..., regulation of RNA metabolic process, regulation of RNA biosynthetic process, regulation of biosynthetic process, regulation of gene expression, regulation of macromolecule biosynthetic..., regulation of cellular biosynthetic proc..., regulation of cellular macromolecule bio..., regulation of nucleobase-containing comp..., regulation of nitrogen compound metaboli..., regulation of cellular metabolic process, regulation of macromolecule metabolic pr..., regulation of primary metabolic process, transcription, DNA-dependent, regulation of metabolic process, RNA biosynthetic process, nucleic acid metabolic process, nucleic acid binding transcription facto..., sequence-specific DNA binding transcript....

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-18120 MT3275 1445
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Gene Target Differential Expression Distance Expression pvalue Type
Repressed -18 -1.61 0.00067476 Primary.TSS
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ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No 25 0.25 0.589883 CDS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
2074 -
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
15610319 NP_217699.1 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 GSM1426942 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426943 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426944 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3183_B154 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.680000 2.88

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: 0.871015
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 8.75 U
D3I 3 3 3.83 7.68 I
D3U 3 3 3.83 7.36 U
D5I 9 5 6.00 11.41 I
D5U 17 5 6.00 11.14 U
D7I 18 7 8.14 8.82 I
D7U 19 7 8.14 8.30 U
D14I 4 14 15.63 5.02 I
D14U 4 14 15.63 6.26 U
D17I 3 17 19.15 4.91 I
D17U 3 17 19.15 4.96 U
D21I 4 21 23.23 5.70 I
D21U 4 21 23.23 5.53 U
D24I 3 24 26.60 5.56 I
D24U 3 24 26.60 5.63 U
D28I 4 28 30.61 5.26 I
D28U 4 28 30.61 6.03 U