ENCODE The ENCODE Project Consortium EBI is an

ENCODE The ENCODE Project Consortium EBI is an Outstation of the European Molecular Biology Laboratory.

Production

Tier 1: GM 12878 K 562 H 1 -ESC Tier 2: Hepg 2 Hela S 3 HUVEC

Production

ENCODE production (All Methods)

Chip-seq

Zoom in on High Coverage methods

Basic Processing Anshul Kundaje, Qun’hua Li. Steve Wilder, Ben Brown, Joel Rozowsky, Felix Schlesinger EBI is an Outstation of the European Molecular Biology Laboratory.

Nice Graphic display of pipeline, IDR, Motifs …. TO BE GENERATED….

Graphic of IDR on non-Chipseq RNA Graphic Dnase-Seq Graphic

IDR Element Set

IDR Element Set

Overall Element summary

“Expected” Discovery and Biology Javier Herrero, Xianjun Dong, Zhiping Weng, Mark Gerstein, Bob Altschuler, Tim Reddy EBI is an Outstation of the European Molecular Biology Laboratory.

Accurate and quantitative prediction of transcription from histone data

There is a diversity of constraint and population level selection on functional elements Bob’s Scatter plot Javier’s information Content vs constrain

Transcription Factors are very different One example difference Screen Shot Of Factor. Book

Transcription Factors have allele specific signals Example Correlation Example

Anti-correlation is very rare; uncorrelated does occur Uncorrelated Anti-correlation H 3 K 27 me 3 vs RNA?

“Less Expected” Biology and Discovery Michael Hoffman, Jason Ernst, Anshul Kundaje, Chao Cheng, Manolis Kellis, Mark Gerstein EBI is an Outstation of the European Molecular Biology Laboratory.

Unbiased, annotation free, generative models Well understood: TSS, Gene Start, Gene Bodies Segmentation Confusion plot Reassuringly Interesting “Enhancers” (2 states) Insulators Definitely There, Unexpected Specific Gene End ? Sub-classification of Repeats

Comparison to Methylation as example

Further sub-divison by Self Organising Maps Ali’s Pictures, GO term enrichment

Ability to find Enchancers in a directed, discriminative way Sophisticiated (Anshul, chao) Less Sophisticiated (Jim)

Networks

Impact on Understanding Variation EBI is an Outstation of the European Molecular Biology Laboratory.

Overall Enrichment of GWAS hits Ross’s Diagrams

Clustering of GWAS wrt to Cell Lines John’s Cluster

Clustering of GWAS vs TFs Pick out Example

Zoom into one Locus

Personal Genome interpretation GM 12878: Mapping Analysis How many more “interesting” SNPs do we find GM 12878, Personalised Analysis Peak calling on a personalised genome

Thanks Slide

Poster Numbers and Paper