The ENCODE Encyclopedia and Variant Annotation … › Multimedia › Slides ›...

The ENCODE Encyclopedia13 13 amp13

Variant AnnotaMon Using 13 RegulomeDB and HaploReg13

Jill E Moore13 13Weng Lab

University of MassachuseOs Medical School13 October 10 201513

 

 

     

      

Wherersquos the Encyclopedia13

bull 13

ENCODE Encyclopedia Of DNA Elements13

bull So far ENCODE data producers have generated thousands of experiments in humans 13 -shy‐ 200+ DNase-shy‐seq13 -shy‐ 800+ TranscripMon Factor (TF) ChIP-shy‐seq13 -shy‐ 300+ Histone Mark ChIP-shy‐seq13 -shy‐ RNA-shy‐seq RNA-shy‐binding DNAme13

bull 13

How do we13 -shy‐-shy‐

Integrate different experiments and assays13 Find funcMonal annotaMons13

-shy‐ Build and visualize the encyclopedia13

 

 

 

 

 

 

 

Genomic AnnotaMons13

bull Gene expression13

13TranscripMon start sites (TSS)bull

bull Uniformly processed peaks from DNase-shy‐seq histone mark ChIP-shy‐seq and TF ChIP-shy‐seq13

bull 3D chromaMn contacts from Hi-shy‐C and ChIA-shy‐PET13

bull Candidate enhancers and promoters13

bull Semi-shy‐automated genome annotaMons (ChromHMM and Segway)13

bull Target genes of regulatory elements13

 

 

 

 

 

 

 









 

 

 

 

 

Step 1 Define DNase Master Peaks (MPs)

Master peaks13 13 bull Are a set of unique non-shy‐overlapping peaks13 13 bull Are a ldquorepresentaMverdquo peak in a region of overlapping peaks1313 bull Span all datasets 13 bull CollecMvely cover ~20 of the genome13

bull Incorporates ENCODE and Roadmap DNase data13

13

Step 1 Define DNase Master Peaks (MPs)Peaks present13 across cell typesin same region Master peak13 (DNase hypersensive region)

cell type 1 10

10cell type 2 8 30

cell type 3 48 8hellip 13 merge

hellip 35 48

35

13 30hellip 9

hellip 11 9cell type N 11

Master peak file created by Stam lab (UW)

 

 

Step 2 Separate DNase MPs by 13 GeneMc Context

DNase master peaks are separated into 13 13 bull TSS-shy‐proximal = within a 2kb window centered on any

GENCODE V19 transcripMon start site (TSS)13 13 bull TSS-shy‐distal = all other peaks13

 

 

 

 

Step 3 Annotate DNase MPs

bull Intersect with TF ChIP-shy‐seq peaks from all cell types13

bull Enrichment in histone mark signal13

-shy‐ For each master peak we calculated histone signal in a 1000 bp window centered on the peak13

13 -shy‐ We converted signal percenMle using a background

distribuMon calculated from randomly chosen 1000-shy‐bp genomic regions (excluding DNase peaks and ENCODE blacklist regions)13

enrichment13

Enrichment of TSS-shy‐distal DNase MPs in GM12878with H3K27ac Signal from GM1287813

peaks

DNase Peaks (n=171028)13 Random Regions (n=171028)13

Background 95th PercenMle 171 13

Enrichment13

 

 

 

 

SelecMon of Histone Marks

bull H3K4me3 -shy‐ enriched at acMvely transcribed promoters13 13 bull H3K9ac -shy‐ enriched at promoters and enhancers13 13 bull H3K27ac enriched at acMve enhancers13 13 bull H3K4me1 -shy‐ enriched at enhancers (both acMve and poised) 13

 

 

 

 

 

 

Current AnnotaMons

bull Proximal Regulatory Elements = proximal DNase MPs13

bull Distal Regulatory Elements = distal DNase MPs13 13 bull Proximal TF Binding = proximal DNase MPs + TF peaks13

bull Distal TF Binding = distal DNase MPs + TF peaks13

bull Candidate Promoters = proximal DNase MPs + enrichment in histone mark13

bull Candidate Enhancers = distal DNase MPs + enrichment in histone mark13

13

How can I access these annotaMons13

wwwencodeprojectorg13




hOpswwwencodeprojectorgfiles ENCFF076KTTdownload ENCFF076KTTbigBed13

UCSC Genome Browser13


 

 

 

 


Other useful tracks13 13 bull UCSC Genes (RefSeq GenBank CCDS Rfam tRNAs amp

ComparaMve Genomics)13 13 bull GENCODE Gene AnnotaMon Tracks13 13 bull Integrated RegulaMon from ENCODE Tracks13 13 bull Genome SegmentaMons from ENCODE (ChromHMM

Segway)13

WashU Epigenome Browser13


13

 

 

 

Genome Browser Links13

bull UCSC Custom tracks13 hOpgenomeucsceducgi-shy‐binhgTracksdb=hg19amphgtcustomText=hOpzlab-shy‐trackhubumassmededuencyclopediaucsc_trackhubtxt13 13

bull UCSC Track Hub13 hOpzlab-shy‐trackhubumassmededuencyclopediav1hubtxt13 13 hOpzlab-shy‐trackhubumassmededuencyclopediav1genometxt13 13 hOpzlab-shy‐trackhubumassmededuencyclopediav1hg19trackDbtxt13 13

bull WashU Hammock tracks13 hOpepigenomegatewaywustledubrowsergenome=hg19ampdatahub=hOp zlab-shy‐trackhubumassmededuencyclopediawashu_trackhubtxt13

hOpwikiwubrowseorgHammock13

 

 

 

Future DirecMons13

bull Open-shy‐source codebase13 13 bull Generate mouse annotaMons13 13 bull Add more data13

131313-shy‐ Refine use of TF data13 RNA-shy‐seq13 3D contacts (ChIA-shy‐PET and Hi-shy‐C)13 ChromHMM and Segway13 Target gene predicMon13

Variant AnnotaMon UsingRegulomeDB and HaploReg13

13

 

 

 

MoMvaMon13

bull The majority of variants reported by GWAS are in noncoding regions of the genome13

bull The variant reported by the GWAS (leadtagged variant) may not be causal but is in high linkage disequilibrium with the casual

13variant

bull Using data from ENCODE we can annotate noncoding regions of the genome and predict the funcMon of disease associated noncoding variants13

13Variant AnnotaMon Tools

h=pwwwregulomedborg

h=pwwwbroadinstuteorgmammalshaploreghaploregphp

h=pregulomestanfordeduGWAS13

13

Acknowledgements13

ENCODE ConsorMum13 Weng LabBrad Bernstein13Zhiping Weng13 Ross Hardison13Michael Purcaro13 Mark Gerstein13 Sowmya Iyer13 Data ProducMon Groups13 Jie Wang13

Arjan van der Velde 13 13

Stam Lab13 John Stamatoyannopoulos 13 Bob Thurman13 Richard Sandstrom13

 

 

     

      

Wherersquos the Encyclopedia13

bull 13

ENCODE Encyclopedia Of DNA Elements13

bull So far ENCODE data producers have generated thousands of experiments in humans 13 -shy‐ 200+ DNase-shy‐seq13 -shy‐ 800+ TranscripMon Factor (TF) ChIP-shy‐seq13 -shy‐ 300+ Histone Mark ChIP-shy‐seq13 -shy‐ RNA-shy‐seq RNA-shy‐binding DNAme13

bull 13

How do we13 -shy‐-shy‐

Integrate different experiments and assays13 Find funcMonal annotaMons13

-shy‐ Build and visualize the encyclopedia13

 

 

 

 

 

 

 









 

 

 

 

 

 

 









 

 

 

 

 




13


cell type 1 10

10cell type 2 8 30


hellip 35 48

35

13 30hellip 9



 

 




 

 

 

 







enrichment13


peaks



Enrichment13

 

 

 

 



 

 

 

 

 

 

Current AnnotaMons






13









 

 

 

 




Segway)13



13

 

 

 






 

 

 

Future DirecMons13




13

 

 

 

MoMvaMon13



13variant



h=pwwwregulomedborg



13

Acknowledgements13




 

 

 

 

 

 

 









 

 

 

 

 

 

 









 

 

 

 

 




13


cell type 1 10

10cell type 2 8 30


hellip 35 48

35

13 30hellip 9



 

 




 

 

 

 







enrichment13


peaks



Enrichment13

 

 

 

 



 

 

 

 

 

 

Current AnnotaMons






13









 

 

 

 




Segway)13



13

 

 

 






 

 

 

Future DirecMons13




13

 

 

 

MoMvaMon13



13variant



h=pwwwregulomedborg



13

Acknowledgements13





cell type 1 10

10cell type 2 8 30


hellip 35 48

35

13 30hellip 9



 

 




 

 

 

 







enrichment13


peaks



Enrichment13

 

 

 

 



 

 

 

 

 

 

Current AnnotaMons






13









 

 

 

 




Segway)13



13

 

 

 






 

 

 

Future DirecMons13




13

 

 

 

MoMvaMon13



13variant



h=pwwwregulomedborg



13

Acknowledgements13




 

 




 

 

 

 







enrichment13


peaks



Enrichment13

 

 

 

 



 

 

 

 

 

 

Current AnnotaMons






13









 

 

 

 




Segway)13



13

 

 

 






 

 

 

Future DirecMons13




13

 

 

 

MoMvaMon13



13variant



h=pwwwregulomedborg



13

Acknowledgements13




 

 

 

 



 

 

 

 

 

 

Current AnnotaMons






13









 

 

 

 




Segway)13



13

 

 

 






 

 

 

Future DirecMons13




13

 

 

 

MoMvaMon13



13variant



h=pwwwregulomedborg



13

Acknowledgements13












 

 

 

 




Segway)13



13

 

 

 






 

 

 

Future DirecMons13




13

 

 

 

MoMvaMon13



13variant



h=pwwwregulomedborg



13

Acknowledgements13






13

 

 

 






 

 

 

Future DirecMons13




13

 

 

 

MoMvaMon13



13variant



h=pwwwregulomedborg



13

Acknowledgements13




 

 

 

Future DirecMons13




13

 

 

 

MoMvaMon13



13variant



h=pwwwregulomedborg



13

Acknowledgements13





13

 

 

 

MoMvaMon13



13variant



h=pwwwregulomedborg



13

Acknowledgements13




 

 

 

MoMvaMon13



13variant



h=pwwwregulomedborg



13

Acknowledgements13





h=pwwwregulomedborg



13

Acknowledgements13





13

Acknowledgements13




The ENCODE Encyclopedia and Variant Annotation … › Multimedia › Slides ›...

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