Rv3744

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3744 nmtR CDS 4195440 4195802 + 363 120 TRUE

Rv3744 () is predicted to be co-regulated in modules bicluster_0168 with residual 0.39 and bicluster_0299 with residual 0.50.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.25 and 0.37 for bicluster_0168 and 0.00 and 48.00 for bicluster_0299 respectively.

These modules are enriched for following go terms: .

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-18201 MT3852 1708
Displaying 1 - 2 of 2
Gene Target Differential Expression Distance Expression pvalue Type
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 13 -0.2 0.811105 CDS
Induced -54 2.08 2.96e-17 Primary.TSS
Displaying 1 - 5 of 5
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulatory protein
Induced -34 1.54 0.000000000016 Primary.TSS
Induced -54 2.08 2.96e-17 Primary.TSS
transcriptional regulator, ArsR family
No -39 -0.08 0.720415 Primary.TSS
Histone protein Lsr2
No -36 0.5 0.119946 Primary.TSS
DNA-binding response regulator TrcR
No -44 0.2 0.770957 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY ARSR-FAMILY] transcriptional regulatory protein ArsR-family
Operon # Operon
2445
PATRIC Locus Tag Enzyme Name Transcriptomics
NA
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
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 GSM1427032 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427033 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427034 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3744_B642 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.920000 1.21

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: 0.000000200308
p-value INH: 0.863117
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.07 U
D3I 3 3 3.83 14.27 I
D3U 3 3 3.83 13.89 U
D5I 9 5 6.00 14.13 I
D5U 17 5 6.00 13.73 U
D7I 18 7 8.14 14.71 I
D7U 19 7 8.14 13.72 U
D14I 4 14 15.63 13.27 I
D14U 4 14 15.63 12.19 U
D17I 3 17 19.15 12.53 I
D17U 3 17 19.15 11.29 U
D21I 4 21 23.23 13.14 I
D21U 4 21 23.23 11.93 U
D24I 3 24 26.60 12.54 I
D24U 3 24 26.60 11.24 U
D28I 4 28 30.61 13.06 I
D28U 4 28 30.61 11.84 U