Rv2827c

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2827c CDS 3134596 3135483 - 888 295 TRUE

Rv2827c () is predicted to be co-regulated in modules bicluster_0395 with residual 0.54 and bicluster_0546 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 760.00 for bicluster_0395 and 0.00 and 0.21 for bicluster_0546 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 4 of 4
Gene Target Differential Expression Distance Expression pvalue Type
DNA-binding response regulator
Repressed -53 -1.01 0.0000000889 Primary.TSS
Methylmalonyl-CoA mutase (EC 5.4.99.2)
No -48 -0.04 0.950474 CDS
Induced 61 3.68 2.8026e-45 Primary.TSS
dTDP-glucose 4,6-dehydratase (EC 4.2.1.46)
No -65 -0.06 0.818237 Primary.TSS
Displaying 1 - 6 of 6
ChipSeq TF Differential Expression Distance Expression pvalue Type
DNA-binding response regulator TrcR
No 33 -0.2 0.809678 Primary.TSS
Induced 61 3.68 2.8026e-45 Primary.TSS
HTH-type transcriptional regulator
No 35 0.09 0.834859 Primary.TSS
transcriptional regulator, ArsR family
Induced 39 1.1 0.000000000226 Primary.TSS
Histone protein Lsr2
No 27 0.4 0.313802 Primary.TSS
No 43 0.02 0.957248 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
Putative uncharacterized protein
Operon # Operon
1854 -
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
15609964 NP_217343.1 Run
GO:0040007

growth

growth

Details: 
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO Category: 
biological_process
621
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 GSM1426877 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426878 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426879 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2827c_B627 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: 0.0000000113837
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.09 U
D3I 3 3 3.83 14.04 I
D3U 3 3 3.83 14.01 U
D5I 9 5 6.00 14.09 I
D5U 17 5 6.00 14.07 U
D7I 18 7 8.14 13.88 I
D7U 19 7 8.14 14.36 U
D14I 4 14 15.63 11.87 I
D14U 4 14 15.63 13.86 U
D17I 3 17 19.15 10.47 I
D17U 3 17 19.15 13.79 U
D21I 4 21 23.23 10.08 I
D21U 4 21 23.23 14.07 U
D24I 3 24 26.60 8.38 I
D24U 3 24 26.60 14.01 U
D28I 4 28 30.61 8.30 I
D28U 4 28 30.61 14.38 U