Morgane Thomas-Chollier - Ecole Normale Supérieure        M2 ENS - September 2015

Session 5: ChIP-seq secondary analysis = what to do with a list of peaks ?

The goal of this exercise is to perform analyses on list of peaks. You will first discover putative binding motifs for transcription factors and then perform a functional analysis of the peaks.

Motif discovery with peak-motifs

You will use here the program peak-motifs to discover motifs within your peaks.
You will follow this protocol: "A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs" by Thomas-Chollier et al, Nature Protocols (2012) PDF As use case, you will not use the sequences of Drosophila, but your set of peaks for the Oct4 factor.

  1. Obtain the sequences corresponding to your peaks. Use the program fetch sequences in RSAT
  2. Follow the complete protocol (remember to read the BOX sections as well)

    3. Question
    Interpret your results using the section "study case 2" in Anticipated results.

  3. Re-run the program by using the peak summits +/-200bp. You will need to use bedtools slopbed to first obtain the genomic coordinates, and then obtain the sequences.

    4. Question
    Do you see the same results ?


Peak annotation (optional)

Here, you will use the online program GREAT to perform functional analysis of your set of peaks.
  1. In the UCSC genome browser, click on the top menu Table browser
  2. select your custom track, and check "output to GREAT" and submit

Question
Does this analysis make sense in the context on the studied factor ?

Morgane Thomas-Chollier - Ecole Normale Supérieure        mthomas[at]biologie.ens.fr