Enrichment analysis

There are certain characteristic elements associative to active enhancers such as: open-chromatin, few histone modifications, 3D-interaction data and experimental evidances etc. In order to provide support for potential regulatory activity of these in-silico predicted enahncers using GEP, we propose enrichment of these elements in predicted enhancers.

Overlap with enhancers

See the overlap of characteristic elements with predicted enhancers.

• Necessary files

  • Enhancer bed-file: A three column bed file
  • List: A list containing file path and name of the characteristic elements
  • outputFolder

Run:

perl votingScore.pl --chrSize <enhancer bedFile> --l <list> --o <outFolder>

Enrichment test

To see the significance of the overlap, we propose a enrichment test. In this test, we consider estimating the distribution of base pair overlap in randomized genomes 1000 times. If the P-value is less than 0.05, we consider the enrichment of characteristic element as “significant” in enhancers.

• Necessary files

  • Enhancer bed-file
  • gFile: A tab-delimited file with Chromosome and size
  • List: A list containing file path and name of the characteristic elements
  • outputFolder
  • outFileName

Run:

Rscript enrichmentAnalysis.R <enhancer bedFile> <gFile> <list> <outputFolder> <outFileName>

Output

Visit Enrichment analysis for output