RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes View Full Text


Ontology type: schema:Chapter      Open Access: True


Chapter Info

DATE

2016-08-25

AUTHORS

Jaime A. Castro-Mondragon , Claire Rioualen , Bruno Contreras-Moreira , Jacques van Helden

ABSTRACT

In this protocol, we explain how to run ab initio motif discovery in order to gather putative transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP-seq experiments. The protocol starts from a set of peak coordinates (genomic regions) which can be either downloaded from ChIP-seq databases, or produced by a peak-calling software tool. We provide a concise description of the successive steps to discover motifs, cluster the motifs returned by different motif discovery algorithms, and compare them with reference motif databases. The protocol is documented with detailed notes explaining the rationale underlying the choice of options. The interpretation of the results is illustrated with an example from the model plant Arabidopsis thaliana. More... »

PAGES

297-322

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-4939-6396-6_19

DOI

http://dx.doi.org/10.1007/978-1-4939-6396-6_19

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1041698723

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27557775


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