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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 [email protected]
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