Rv3440c

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3440c CDS 3859665 3859976 - 312 103 FALSE

Rv3440c () is predicted to be co-regulated in modules bicluster_0024 with residual 0.54 and bicluster_0301 with residual 0.61.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 1.30 and 1.50 for bicluster_0024 and 0.00 and 4.40 for bicluster_0301 respectively.

These modules are enriched for following go terms: divalent metal ion transport, divalent inorganic cation transport, transition metal ion transport, divalent inorganic cation transmembrane ....

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 10/16/2017 - 15:33
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-17950 MT3545 975
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No -22 -0.31 0.186534 CDS
Transcriptional regulatory protein
Induced -39 0.65 0.000391214 CDS
Motif 1 Motif 2 Residual
bicluster_0024
e.value: 
1.3
Motif Bicluster: 
e.value: 
1.5
Motif Bicluster: 
0.54
bicluster_0301
e.value: 
0.00091
Motif Bicluster: 
e.value: 
4.4
Motif Bicluster: 
0.61
Product (LegacyBRC) Product (RefSeq)
Putative uncharacterized protein
Operon # Operon
2249 -
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
15610576 NP_217957.1 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.
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.140000 0.87

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:
p-value INH: