ColoWeb: a resource for analysis of colocalization of genomic features
LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor
Cited from COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets
"In order to compare the in vivo overlap with the expected (background) overlap, an overlap analysis was performed for the frequent motif patterns for which genome-wide data was available. The expected overlap was measured by randomly permuting (1000 times) the same number of regions bound by one TF through the genome and the mean overlap was subsequently calculated. The significance of the observed compared to the expected overlap was calculated by assuming that the overlap follows a Poisson distribution."
CGATOxford Tools
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