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Methods Mol Biol. 2016;1482:279-95. doi: 10.1007/978-1-4939-6396-6_18.

RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes.

Author information

1
Estación Experimental de Aula Dei-CSIC, Av. Montañana 1.005, 50059, Zaragoza, Spain. bcontreras@eead.csic.es.
2
Fundación ARAID, calle María de Luna 11, 50018, Zaragoza, Spain. bcontreras@eead.csic.es.
3
INSERM, U1090 TAGC, Aix Marseille University, U1090 TAGC, Marseille, 13288, France.
4
Estación Experimental de Aula Dei-CSIC, Av. Montañana 1.005, 50059, Zaragoza, Spain.

Abstract

The plant-dedicated mirror of the Regulatory Sequence Analysis Tools (RSAT, http://plants.rsat.eu ) offers specialized options for researchers dealing with plant transcriptional regulation. The website contains whole-sequenced genomes from species regularly updated from Ensembl Plants and other sources (currently 40), and supports an array of tasks frequently required for the analysis of regulatory sequences, such as retrieving upstream sequences, motif discovery, motif comparison, and pattern matching. RSAT::Plants also integrates the footprintDB collection of DNA motifs. This protocol explains step-by-step how to discover DNA motifs in regulatory regions of clusters of co-expressed genes in plants. It also explains how to empirically control the significance of the result, and how to associate the discovered motifs with putative binding factors.

KEYWORDS:

Cluster; Co-expression; DNA motif; Position-weight matrix; Upstream sequence

PMID:
27557774
DOI:
10.1007/978-1-4939-6396-6_18
[Indexed for MEDLINE]

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