Parameters for motif searches

Sequence motifs were extracted from the entire robust FANTOM5 CAGE-TSS (Forrest et al. 2014, Nature) or bidirectional CAGE enhancer datasets (Anderson et al. 2014, Nature) or tissue- or cell type-specific enhancer facets (as descibed in Anderson et al. 2014, Nature) using HOMER (version 3), a suite of tools for motif discovery and next-gen sequencing analysis developed by Christopher Benner (Integrative Genomics Core, Salk Institute, San Diego).
The programs findMotifGenome.pl, compareMotifs.pl and findKnownMotifs were slightly modified to generate a non-standard html output, add sample information and create additional options for thresholding. Known motif enrichment was determined using all available HOMER-derived vertebrate PWM and standard parameters.

Parameters for de novo searches in complete enhancer/promoter sets

Parameters for de novo searches in cell type- or tissue-specific enhancer sets

Known Motif PWMs used to match de novo-derived motifs

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