Rv0339c POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0339c POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN CDS 405950 408448 - 2 499 832 TRUE

Rv0339c (POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN) is predicted to be co-regulated in modules bicluster_0161 with residual 0.58 and bicluster_0414 with residual 0.45.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 1,500.00 and 11,000.00 for bicluster_0161 and 65.00 and 550.00 for bicluster_0414 respectively.

These modules are enriched for following go terms: purine-containing compound biosynthetic ... .

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-1.025 65 408465 408400 408448
Displaying 1 - 10 of 10
Gene Target Differential Expression Distance Expression pvalue Type
Partial REP13E12 repeat protein
No 9 0.49 0.276826 Antisense.TSS
3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11)
Repressed 42 -1.42 5.78e-16 Primary.TSS
PPE family protein
No 48 -0.41 0.344431 CDS
SSU ribosomal protein S4p (S9e)
No -73 0.05 0.922513 Antisense.TSS
Partial REP13E12 repeat protein
No 39 0.29 0.541347 Antisense.TSS
No -20 -0.23 0.563399 Primary.TSS
PE family protein
No 40 0.04 0.977889 CDS
Cell division protein DivIC (FtsB), stabilizes FtsL against RasP cleavage
No -56 0.01 0.989659 CDS
No -32 -0.18 0.788426 Internal.TSS
No -41 -0.18 0.788426 CDS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
234
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
15607480 NP_214853.1 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 GSM1426465 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426466 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426467 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0339c_B412 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.360000 1.14

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: 0.000000918846
p-value INH: 0.600311
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.61 U
D3I 3 3 3.83 12.62 I
D3U 3 3 3.83 12.76 U
D5I 9 5 6.00 12.30 I
D5U 17 5 6.00 12.68 U
D7I 18 7 8.14 12.00 I
D7U 19 7 8.14 12.76 U
D14I 4 14 15.63 9.33 I
D14U 4 14 15.63 12.10 U
D17I 3 17 19.15 6.98 I
D17U 3 17 19.15 11.78 U
D21I 4 21 23.23 6.03 I
D21U 4 21 23.23 11.92 U
D24I 3 24 26.60 3.72 I
D24U 3 24 26.60 11.70 U
D28I 4 28 30.61 4.85 I
D28U 4 28 30.61 11.72 U