ECCB'14 - T01 - Analysis of Cis-Regulatory Motifs from High-Throughput Sequence Sets

T01 - Analysis of Cis-Regulatory Motifs from High-Throughput Sequence Sets

-date: Saturday 6th september 2014

-venue : Forum building of the Faculty of Medicine of Strasbourg.

Faculté de Médecine
Forum (Building)
4, rue Kirschleger
67085 Strasbourg

-short description: This tutorial aims at introducing the theoretical principles and giving practical skills to use specialized software tools to extract motifs from full-scaled NGS datasets (typically covering tens of Mb).

-name of the chair(s): Jacques van Helden & Morgane Thomas-Chollier

-contact e-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Note: bring your own laptop

Motivation

Next Generation Sequencing led to the development of novel methods (ChIP-seq, FAIRE-seq, clip-seq, ) to acquire massive data about diverse signals involved in genome regulation and function (cis-regulation, chromatin conformation, RNA maturation, recombination, replication, …). Extracting relevant information from the raw data requires not only specialized software tools, but also a good understanding of their principles and parameters.

Goals

In this tutorial we will demonstrate how to analyze ChIP-seq data using the Regulatory Sequence Analysis Tools (http://www.rsat.eu/), via their different ways of access: web-interface, command-line, and web-services.

This tutorial aims at introducing the theoretical principles and giving practical skills to use specialized software tools to extract motifs from full-scaled NGS datasets (typically covering tens of Mb).

Topics covered

The tutorial will be organized in 2 half days:

1) Analysis of cis-regulatory elements with the Regulatory Sequence Analysis Tools (RSAT): methods and website utilization (http://www.rsat.eu/).

2) Using RSAT in command-line and via web services (SOAP/WSDL).

Topics

Motif discovery in NGS peak sets.
Impact of the background models.
Comparison between motifs.
Motif enrichment in peak sequences.
Evaluating the quality of motifs extracted from NGS peaks.
Building control sets to estimate the rates of false positives.

Topics not covered

Other steps for the analysis of ChIP-seq data (e.g. read mapping, peak calling, functional enrichment of peaks, other tools for pattern discovery and matching).

Intended audience and possible prerequisites

The course is addressed to bioinformaticians and biologists. The afternoon will require being familiar with the Unix shell (Linux) and basic programming skills (Perl or Python) to implement clients for web services.

In practice:

Participants will need to bring their own laptop
All command-line programs will be run on the IFB (Institut Français de Bioinformatique)'s cloud platform managed by Christophe Blanchet (IBCP, Lyon, France). Each participant will be given a (free) account to access this cloud and thereby a fully functional virtual machine with RSAT.
Wireless internet will be available at the conference venue. In the worse case, where the network would become unavailable during the day, we would still be able to give a demo on the teacher laptops.
An indicative reading list will be available a few weeks before the tutorial.
The hands-on will be organized in a cookbook mode: we will distribute protocols explaining the steps to solve selected test cases.
For the practicals, we ensure that there is no need to transfer data from the conference room to the servers.

Presenters:

Jacques van Helden, professor at Aix-Marseille Université (France)

Morgane Thomas-Chollier, associate professor at Ecole Normale Supérieure (France)

Carl Herrmann, Assistant professor in bioinformatics, University Heidelberg (Germany). Previously Associate professor at Aix-Marseille Université (France)

Alejandra Medina-Rivera, Postdoctoral Fellow at SickKids Research Institute, Toronto (Canada)

Do not hesitate to contact us ! e-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Reading list:

main reference is the general description of the RSAT tools:
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W86-91. doi: 10.1093/nar/gkr377.
RSAT 2011: regulatory sequence analysis tools.
Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, van Helden J.
http://www.ncbi.nlm.nih.gov/pubmed/21715389

two articles about RSAT peak-motifs

Nucleic Acids Res. 2012 Feb;40(4):e31. doi: 10.1093/nar/gkr1104. Epub 2011 Dec 8.
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets.
Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J.
http://www.ncbi.nlm.nih.gov/pubmed/22156162

Nat Protoc. 2012 Jul 26;7(8):1551-68. doi: 10.1038/nprot.2012.088.
A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.
Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J.
http://www.ncbi.nlm.nih.gov/pubmed/22836136

For the peak enrichment in sites of the immunoprecipitated factor, we will use RSAT matrix-quality

Nucleic Acids Res. 2011 Feb;39(3):808-24. doi: 10.1093/nar/gkq710. Epub 2010 Oct 4.
Theoretical and empirical quality assessment of transcription factor-binding motifs.
Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J.
http://www.ncbi.nlm.nih.gov/pubmed/20923783

As we will not cover the other steps for the analysis of ChIP-seq data (e.g. read mapping, peak calling, functional enrichment of peaks, other tools for pattern discovery and matching), we encourage the participants not familiar with these steps to read the following review:

Bailey, T. et al. Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9, e1003326 (2013).

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326