1 Procedure

AME (Analysis of Motif Enrichment; tool in MEME Suite) is used to do motif enrichment analysis. For a given motif set and a set of sequences, test whether a motif occurs significantly in the sequences.

Some windows were extracted and fed to AME to perform motif enrichment analysis (search in JASPAR 2016 vertebrates). Here top 0.1% windows that decrease the score most in positive sequences and top 0.1% windows that increase the score most in negative sequences and randomly selected windows in positive sequences were analyzed respectively.

Results of randomly selected windows can be found: - E081 top 0.1% positive, - E081 random positive, - E081 top 0.1% negative, - Noonan top 0.1% positive, - Noonan random positive, - Noonan top 0.1% negative, - hNSC-50 top 0.1% positive, - hNSC-50 random positive, - hNSC-50 top 0.1% negative,

2 GO term analysis of hitted TF

Here JASPAR TFs is selected as the background protein list.

library(pander)
pandoc.table(tf.counts)

## Warning in .local(object, test.stat, ...): No enrichment can pe performed - there are no feasible GO terms!

panderOptions('knitr.auto.asis', FALSE)
panderOptions('table.split.table', Inf)
for (i in names(go.results)){
  cat('\n')
  cat("## ", i, "\n")
  pander(go.results[[i]])
  cat('\n')
}