What it does

RnaChipIntegrator was designed to integrate genes/transcripts from expression analysis (RNA-seq, microarrays) with ChIP-seq binding regions, however it is flexible enough to allow the comparison of any genome coordinate based data sets.

RnaChipIntegrator answers the questions:

  • “Which genes are close to each of my ChIP-seq regions?”, and
  • “Which ChIP-seq regions are close to each of my genes?”.

The first data set, called ‘genes’, is strand specific and the genome coordinates correspond to the transcription start site (TSS) and transcription end site (TES), depending on the strand.


For strand and genome coordinates:

  • The start coordinate of a gene on the forward or ‘+’ strand relates to the TSS;
  • The start coordinate of a gene on the reverse or ‘-‘ strand relates to the TES.

This is primarily gene or transcript annotation for the whole genome. However, other non-gene features, such as CpG islands, can be used.

The second data set we call ‘peaks’ are strand non-specific, including only the start and end coordinate. This is primarily the coordinates of ChIP-seq binding regions (a.k.a. peaks).

See the Input files section for more information about the input file formats.

Example use cases (‘gene’ versus ‘peak’) include:

  • RNA-seq expressed genes versus ChIP-seq binding regions
  • Microarray expressed genes versus ChIP-chip binding regions
  • Total gene annotation versus ChIP-seq binding regions
  • Gene promoters versus CpG island annotation