Chip-seq data analysis: from quality check to motif discovery and more

Lausanne, 27 April - 1 May 2015

Data reproduction exercises

Exercise Publication details Relevant figure
Cross-correlaiton analysis Landt et al. 2012, ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research 22, 1813-1831. PMID 22955991
Irreproducible Discovery Rate (IDR) Landt et al. 2012, ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research 22, 1813-1831. PMID 22955991
Alignment of MNase tags around NFKB sites Gaffney et al. 2012, Controls of nucleosome positioning in the human genome. PLoS Genetics. 8: e1003036. PMID 23166509
Variation in Drosophila transcription factor binding sites Spivakov et al. 2012. Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol. 13:R49. PMID 22950968
Epigenetic variation across promoter types Nozaki et al. 2011. Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification BMC Genomics, 12:416 PMID 21846408
Nucleosome signals around promoter types FANTOM Consortium 2014. A promoter-level mammalian expression atlas. Nature 507, 462-470, 2014. PMID 24670764
Nucleosome organization around YY1 sites Wang et al. 2012. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors, Genome Research 22, 1798-1812. PMID 22955990
Peak list evaluation - motif enrichment test Wilbanks & Facciotti 2010. Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One. 7:e41389. PMID 20628599