Rv0348

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0348 CDS 418293 418946 + 654 217 TRUE

Rv0348 () is predicted to be co-regulated in modules bicluster_0066 with residual 0.56 and bicluster_0466 with residual 0.57.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 47.00 and 3,300.00 for bicluster_0066 and 0.57 and 9,200.00 for bicluster_0466 respectively.

These modules are enriched for following go terms: glycerol ether metabolic process, ether metabolic process, protein disulfide oxidoreductase activit..., disulfide oxidoreductase activity potassium ion transport, ion transmembrane transporter activity, substrate-specific transmembrane transpo..., substrate-specific transporter activity, transmembrane transporter activity, cation transmembrane transporter activit....

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 3 of 3
Gene Target Differential Expression Distance Expression pvalue Type
Repressed -25 -0.86 0.0409565 Internal.TSS
Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8)
No 39 0.16 0.809279 Internal.TSS
Transcriptional regulator kstR (Rv3574), TetR family
No -3 0.37 0.384637 Primary.TSS
Displaying 1 - 5 of 5
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, ArsR family
No -59 -0.03 0.930292 CDS
No -25 0.46 0.245306 Antisense.TSS
Transcriptional regulator, TetR family
No -87 0.15 0.826556 CDS
No 22 0.46 0.245306 Internal.TSS
transcriptional regulator, ArsR family
No -47 0.5 0.035518 CDS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [Putative uncharacterized protein] transcriptional regulatory protein
Operon # Operon
240 - -
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
15607489 NP_214862.1 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 GSM1426468 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426469 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426470 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0348_B413 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.530000 0.22

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: 0.0199422
p-value INH: 0.873582
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.15 U
D3I 3 3 3.83 12.13 I
D3U 3 3 3.83 12.42 U
D5I 9 5 6.00 13.12 I
D5U 17 5 6.00 12.78 U
D7I 18 7 8.14 13.04 I
D7U 19 7 8.14 12.52 U
D14I 4 14 15.63 14.40 I
D14U 4 14 15.63 13.35 U
D17I 3 17 19.15 14.80 I
D17U 3 17 19.15 13.37 U
D21I 4 21 23.23 15.06 I
D21U 4 21 23.23 13.77 U
D24I 3 24 26.60 15.35 I
D24U 3 24 26.60 13.73 U
D28I 4 28 30.61 15.43 I
D28U 4 28 30.61 13.93 U