Rv0078 Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0078 Transcriptional regulator, TetR family CDS 86528 87133 + 606 201 TRUE

Rv0078 (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0115 with residual 0.48 and bicluster_0494 with residual 0.46.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 50.00 and 1,500.00 for bicluster_0115 and 0.68 and 6.50 for bicluster_0494 respectively.

These modules are enriched for following go terms: .

This gene is found to be non-essential for growth on cholesterol.

Mutant available?:

Displaying 1 - 2 of 2
Gene Target Differential Expression Distance Expression pvalue Type
Oxidoreductase
Repressed 39 -1.44 0.000293462 CDS
Transcriptional regulator, TetR family
Induced -23 3.52 1.21e-23 CDS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, ArsR family
Repressed -93 -1.83 0.0000000132 CDS
Transcriptional regulator, ArsR family
No -43 -0.55 0.165464 CDS
Transcriptional regulator, TetR family
Induced -23 3.52 1.21e-23 CDS
Motif 1 Motif 2 Residual
bicluster_0115
e.value: 
50
Motif Bicluster: 
e.value: 
1500
Motif Bicluster: 
0.48
bicluster_0494
e.value: 
0.68
Motif Bicluster: 
e.value: 
6.5
Motif Bicluster: 
0.46
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
53 Rv0078
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
15607220 NP_214592.1 Run
GO:0005886

plasma membrane

plasma membrane

Details: 
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO Category: 
cellular_component
1284
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 GSM1426396 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426397 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426398 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426399 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0078_B399 UCSC Browser Tracks
Quantitative Proteomics Data
Cholesterol Essentiality t-test p-value Cholesterol/Glycerol Ratio
non-essential 0.320000 0.66

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.

Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.26 U
D3I 3 3 3.83 10.64 I
D3U 3 3 3.83 10.07 U
D5I 9 5 6.00 10.46 I
D5U 17 5 6.00 10.42 U
D7I 18 7 8.14 10.64 I
D7U 19 7 8.14 10.29 U
D14I 4 14 15.63 7.18 I
D14U 4 14 15.63 7.70 U
D17I 3 17 19.15 6.00 I
D17U 3 17 19.15 6.70 U
D21I 4 21 23.23 5.52 I
D21U 4 21 23.23 6.89 U
D24I 3 24 26.60 3.71 I
D24U 3 24 26.60 5.16 U
D28I 4 28 30.61 4.71 I
D28U 4 28 30.61 5.64 U