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Introduction to the Second Epigenome Informatics Workshop

Aleksandar Milosavljevic

Epigenomics Data Analysis

and Coordination Center (EDACC)

Presented at the 2nd Epigenome Informatics WorkshopHouston, Texas, September 9th 2010

Announcement

Modules 1-8 will be partially recorded and distributed.

Welcome to the Texas Medical Center

Rice University Baylor College of Medicine

Downtown Houston

Workshop Sponsors and Funders

NIH Epigenomics Roadmap ProjectHypothesis:

Origins of health and susceptibility to disease are, in part, result of epigenetic regulation

Goal:

Transform biomedical research by

• Developing comprehensive reference epigenome maps

• Developing new technologies for epigenomic analyses

(adapted from John Satterlee’s talk March, 2009)

EDACC Data Coordination

Mapping Centers

Health and disease

NewTech.

NovelMarks

NCBI Data Distribution

Workshop purpose

1.Educate participants about the cyberinfrastructure developed at EDACC to support analyses of epigenomic data.

2.Explore ways in which EDACC and REMCs can enable disease projects.

3.Exchange experience in epigenomic data analysis tools and methods.

4.Explore collaborative opportunities. Explore opportunities for collaborative building, analysis and uses of Human Epigenome Atlas

Introductions

EDACC Director Dr. Aleksandar Milosavljevic Modules 1,6,7 EDACC Co-director Dr. Arthur L. Beaudet

Dr. R. Alan Harris Modules 2,3Dr. Cristian Coarfa Modules 4,5,9Dr. Wei LiDr. Robert A. WaterlandMr. Andrew R. Jackson Module 8

Workshop coordinator Ms. Elke Norwig-Eastaugh elken@bcm.edu

Full list of EDACC / BRL members:http://www.brl.bcm.tmc.edu

Self-introduction of workshop participants

Workshop schedule

Workshop schedule

Workshop schedule

NIH Epigenomics Roadmap Initiative

5 100s samples

DNA methylation Histone modificationsChromatin accessibility RNA-seq

50Reference Epigenomes

Disease Epigenomes

Chromatin accessibility

10

Data Flowwww.roadmapepigenomics.org

Creating a Data Commons

Data Level (0-4) definitions

“chip” data “seq” data

Level 0 image reads

Level 1 extracted features mapped reads

Level 2 normalizedintensities

raw signal (read density)

Level 3 epigenomic state of an individual sample

Level 4 results of integrative analyses involving more than one sample

Creating a Data Commons: Metadata Extended

NCBI Short Read Archive XML (SRA-XML)

Data Levels 0-4

Data FlowMapping Centers EDACC

NCBIArchive and Portal

VerifyLevel 1-3analyses

Create Genboree project and verify run data

Reference primaryanalysispipeline

Journal Publication

PerformLevel 4Analyses and publish

NCBI Epigenomics Portalhttp://www.ncbi.nlm.nih.gov/epigenomics

Human Epigenome Atlas Release 1 (June 14th, 2010 based on April 1st , 2010 freeze )

www.epigenomeatlas.org

Assays

SamplesExperiments

Human Epigenome Atlas Release 1www.epigenomeatlas.org

Assays

Human Epigenome Atlas Release 1www.epigenomeatlas.org

Samples

Human Epigenome Atlas Release 1www.epigenomeatlas.org

Experiments

Human Epigenome Atlas Release 1www.epigenomeatlas.org

Samples

Data DownloadsApril - Jul 2010( not including

NCBI ) :

EDACC Aim: Cyberinfrastructure forBuilding, Analyzing and Using the Human Epigenome Atlas

Genboree

Genome-centricdatabases

Users Groups

Roles

Access

Projects

Genboree Workbench

Tools