Rv0880 Transcriptional regulator, MarR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0880 Transcriptional regulator, MarR family CDS 978934 979365 + 432 143 TRUE

Rv0880 (Transcriptional regulator, MarR family) is predicted to be co-regulated in modules bicluster_0305 with residual 0.55 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 , 0.00 and 0.07 for bicluster_0305 and 65.00 and 550.00 for bicluster_0414 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 20
Gene Target Differential Expression Distance Expression pvalue Type
Iron-regulated heparin binding hemagglutinin HbhA (Adhesin)
No -14 -0.21 0.57204 CDS
DNA-directed RNA polymerase beta subunit (EC 2.7.7.6)
No 34 0.03 0.956743 Primary.TSS
Mycofactocin system transcriptional regulator
No 33 0.04 0.963476 CDS
Mycofactocin system small protein
No -14 0.07 0.942248 Primary.TSS
Repressed 31 -2.11 1.65e-16 CDS
No -142 0.2 0.550342 Primary.TSS
DNA-binding response regulator
No -10 -0.01 0.99008 Primary.TSS
No -54 -0.12 0.796636 CDS
Proline-rich antigen homolog
No -104 -0.25 0.720423 Primary.TSS
Polyketide synthase
No -29 -0.21 0.634491 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No results were found
Motif 1 Motif 2 Residual
bicluster_0305
e.value: 
0.000000000067
Motif Bicluster: 
e.value: 
0.069
Motif Bicluster: 
0.55
bicluster_0414
e.value: 
65
Motif Bicluster: 
e.value: 
550
Motif Bicluster: 
0.45
Product (LegacyBRC) Product (RefSeq)
Uncharacterized HTH-type transcriptional regulator Rv0880_MT09031 MarR family transcriptional regulator
Operon # Operon
589 - -
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
15608020 NP_215395.1 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 GSM1426581 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426582 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426583 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0880_B429 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
NA NA

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: 0.572674
p-value INH: 0.860973
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.97 U
D3I 3 3 3.83 11.68 I
D3U 3 3 3.83 12.23 U
D5I 9 5 6.00 10.16 I
D5U 17 5 6.00 10.20 U
D7I 18 7 8.14 9.73 I
D7U 19 7 8.14 9.98 U
D14I 4 14 15.63 7.47 I
D14U 4 14 15.63 9.08 U
D17I 3 17 19.15 5.35 I
D17U 3 17 19.15 8.43 U
D21I 4 21 23.23 4.94 I
D21U 4 21 23.23 8.34 U
D24I 3 24 26.60 2.33 I
D24U 3 24 26.60 7.59 U
D28I 4 28 30.61 4.02 I
D28U 4 28 30.61 7.00 U