TransCistor
TransCistor is a framework for defining and identifying cis-lncRNAs based on enrichment of targets amongst proximal genes.
How it works
TransCistor has two modules; Digital and Analogue
Digital
Estimates the overrepresentation of proximal targets in the lncRNA's TAD
TransCistor utilizies all available TADs (40 for human, 3 for mouse) and provides the harmonic mean of the individual pvalues (hypergeometric test).
Analogue
Calculates if the targets are closer by random change
Estimates the mean distance and compares to random simulations (empirical pvalue)
How to use TransCistor
TransCistor requires one input file ( Gene Regulation File ) and various parameters. The Gene Regulation File is a series of genes and a flag(0,1 or -1) indicating if they are targets and in which direction.
Gene Regulation File format
Tab-separated, two column, headerless file.
First column: gene name or identifier.
Second column: -1/0/+1 for decreasing/unchanged/increasing after lncRNA knock down.
It must contain all genes in the experiment.
Accepted identifiers:
ENSEMBL, SYMBOL, ENTREZID
An example is provided by the known cis-acting lncRNA
UMLILO
.
For the UMLILO example file enter:
FIle Type: ENSEMBL
Species: human
TAD: All
Output name: UMLILO
Chromosome: chr4
TSS location: 73710302
Strand orientation: +
Press
Submit
Additionally, TransCistor allows the use of a custom TAD file.
The custom TAD file format should be space-separated and headerless with three columns:
Chromosome, TAD Start, TAD Stop.
Created in goldlab (https://www.gold-lab.org/). Many people contributed including but not limited to:
Panagiotis Chouvardas, Bhavya Dhaka, Marc Zimmerli, Daniel Hanhart and Mario Moser.
For more info contact: panagiotis.chouvardas@dbmr.unibe.ch and rory.johnson@ucd.ie