Rv0735 RNA polymerase sigma-70 factor

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0735 sigL RNA polymerase sigma-70 factor CDS 827543 828076 + 534 177 TRUE

Rv0735 (RNA polymerase sigma-70 factor) is predicted to be co-regulated in modules bicluster_0167 with residual 0.51 and bicluster_0256 with residual 0.48.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 49.00 for bicluster_0167 and 0.01 and 0.27 for bicluster_0256 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 8 of 8
Gene Target Differential Expression Distance Expression pvalue Type
Type I antifreeze protein
No -23 0.04 0.991782 Primary.TSS
Thioredoxin TrxB1
No 13 -0.3 0.819451 CDS
PROBABLE CONSERVED POLYKETIDE SYNTHASE ASSOCIATED PROTEIN PAPA4
No 48 0.05 0.951764 Antisense.TSS
probable iron binding protein from the HesB_IscA_SufA family
No -35 0.11 0.855718 Primary.TSS
Glycerate kinase (EC 2.7.1.31)
No -57 -0.02 0.988375 Antisense.TSS
No -15 0.05 0.987283 CDS
Membrane alanine aminopeptidase N (EC 3.4.11.2)
No -117 -0.11 0.856311 Primary.TSS
Thiosulfate sulfurtransferase, rhodanese (EC 2.8.1.1)
No -99 0.01 0.995464 CDS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, ArsR family
No -82 0.4 0.132961 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
RNA polymerase sigma factor RNA polymerase sigma factor SigL
Operon # Operon
484
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

RNA polymerase

17
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15607875 NP_215249.1 Run
GO:0005515

protein binding

protein binding

Details: 
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
GO Category: 
molecular_function
135
Total items in this category:  
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 GSM1426543 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426544 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426545 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426543 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426544 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426545 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0735_B426 UCSC Browser Tracks
Rv0735_B565 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.940000 1.66

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.

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: 0.014955
p-value INH: 0.863117
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.98 U
D3I 3 3 3.83 13.54 I
D3U 3 3 3.83 13.28 U
D5I 9 5 6.00 13.97 I
D5U 17 5 6.00 14.15 U
D7I 18 7 8.14 13.33 I
D7U 19 7 8.14 13.67 U
D14I 4 14 15.63 10.39 I
D14U 4 14 15.63 11.93 U
D17I 3 17 19.15 8.55 I
D17U 3 17 19.15 11.24 U
D21I 4 21 23.23 8.27 I
D21U 4 21 23.23 11.50 U
D24I 3 24 26.60 6.18 I
D24U 3 24 26.60 10.84 U
D28I 4 28 30.61 6.45 I
D28U 4 28 30.61 11.08 U