Working Group 3 - Motifs and conservation

Ab-initio motif finding methods (Vlad, Yulia, others)

• Optimizing existing motif
• Finding novel motifs

ChIP-Seq and motif finding

• Motif finding using ChIP-Seq data, or
• Use ChIP-Seq to validate novel TF binding motifs
• TF knockdown CAGE (Morana)

Exo-ChIP gives super-nice motifs (Ben Brown)

Deorphanize TFs

• Ranked list of candidate novel motifs for orphan TFs
• Promoters expressed in a sample → novel motifs → TFs expressed in that sample
• Use motif activity to reduce the number of motifs to look for
• Existing literature in this area?

Distinguish true promoters from other CAGE data

• Timo’s approach

TFBS clusters; combinations of TFs binding near each other

CAGE promoter shapes can be associated with specific motifs

How to use epigenetic data in motif finding

• Cell-type/condition specific
• Narrow the motif search space promoter-by-promoter

Non-TF motif finding

• CAGE signal in the 3’ UTR
• miRNA binding sites in 3’ UTRs
• RNAseq, CAGEscan, RACE to find the extent of the transcript
• motif activity – type calculations applied to miRNAs

Data exchange, mailing list, wiki

• Heated discussions on the mailing lists are encouraged
• Wiki can contain data, detailed descriptions of the methodology

Upload prediction tracks to Zenbu to make them viewable to everybody

• In addition to flat-files on the Wiki

State-specific motifs:

• Ranked list of motifs specific / enriched in specific samples
  • Motif activities for UPDATE_011
  • Motif activities for UPDATE_010