Rv0678

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0678 CDS 778990 779487 + 498 165 TRUE

Rv0678 () is predicted to be co-regulated in modules bicluster_0300 with residual 0.49 and bicluster_0397 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 1.40 for bicluster_0300 and 0.00 and 0.00 for bicluster_0397 respectively.

These modules are enriched for following go terms: tricarboxylic acid cycle enzyme complex, acid-thiol ligase activity, ligase activity, forming carbon-sulfur b... nitrogen compound metabolic process, carbon-oxygen lyase activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Distance to Tuberculist Start Codon Internal TSS New Internal UTR New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.391 122 779112 -131 -7 778988 778981 778990
Displaying 1 - 10 of 268
Gene Target Differential Expression Distance Expression pvalue Type
Serine/threonine-protein kinase PknB (EC 2.7.11.1)
No -27 0.01 0.970235 CDS
2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
No -53 0.58 0.15077 Primary.TSS
No -136 0.27 0.282314 Internal.TSS
No -76 0.27 0.282314 Internal.TSS
Replicative DNA helicase (EC 3.6.1.-) @ intein-containing
No -76 0.29 0.149389 Primary.TSS
Partial REP13E12 repeat protein
No 31 0.01 0.979322 Antisense.TSS
Phosphoheptose isomerase (EC 5.3.1.-)
No -2 0.37 0.263716 CDS
Dihydroflavonol-4-reductase (EC 1.1.1.219)
No 18 -0.03 0.900685 Antisense.TSS
NAD(P) transhydrogenase alpha subunit (EC 1.6.1.2)
No -31 0.25 0.388061 CDS
NAD(P) transhydrogenase alpha subunit (EC 1.6.1.2)
No 66 0.44 0.173086 CDS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No 68 -0.06 0.938606 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0300
e.value: 
0.00000045
Motif Bicluster: 
e.value: 
1.4
Motif Bicluster: 
0.49
bicluster_0397
e.value: 
0.000000000016
Motif Bicluster: 
e.value: 
0.000063
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
Putative uncharacterized protein
Operon # Operon
454
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
15607818 NP_215192.1 Run
GO:0006355

regulation of transcription, DNA-dependent

regulation of transcription, DNA-dependent

Details: 
Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
15
Total items in this category:  
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 GSM1426532 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426533 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426534 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426535 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0678_B352 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.490000 3.45

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: 0.00000010407
p-value INH: 0.0000744403
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.19 U
D3I 3 3 3.83 13.23 I
D3U 3 3 3.83 12.65 U
D5I 9 5 6.00 9.29 I
D5U 17 5 6.00 10.09 U
D7I 18 7 8.14 10.70 I
D7U 19 7 8.14 13.18 U
D14I 4 14 15.63 8.46 I
D14U 4 14 15.63 13.79 U
D17I 3 17 19.15 4.72 I
D17U 3 17 19.15 14.16 U
D21I 4 21 23.23 4.45 I
D21U 4 21 23.23 13.42 U
D24I 3 24 26.60 3.27 I
D24U 3 24 26.60 13.79 U
D28I 4 28 30.61 3.93 I
D28U 4 28 30.61 12.89 U