A website for ChIP data analysis








Chromatin immunoprecipitation (ChIP) is a technology commonly used to map genome-wide protein-DNA interactions. ChIPseek is a tool designed to analyze ChIP data. By integrating HOMER and BEDTools, ChIPseek provides an opportunity for users to analyze the ChIP data without any programing skill. ChIPseek also allows users to define their own parameters to create a subset of dataset for further analysis and download the results. To use ChIPseek requires no knowledge of Linux, programming, no installation and no login. As shown in the demo datasets (demo 1, demo 2), ChIPseek can

  1. annotate the peaks
  2. link to UCSC genome browser
  3. provide pie charts, histograms and bar charts for peak location distribution
  4. apply filter criteria by peak length to get a subset of peaks
  5. apply filter criteria by distance to nearest TSS to get a subset of peaks
  6. apply filter criteria by location of the peaks
  7. apply filter criteria by list(s) of genes
  8. apply filter criteria by GO terms
  9. apply filter criteria by KEGG pathway annotations
  10. compare two datasets
  11. compare dataset with ENCODE transcription factor dataset
  12. identify enriched motif
  13. plot peaks on chromosome ideograms
  14. allow users to download figures or tables

New user is advised to read our tutorial before using ChIPseek.