biodb 2011-05
TRANSCRIPT
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ENCODE Data Available through The UCSC Genome Browser
Materials prepared byMary Mangan, Ph.D.Warren C. Lathe, Ph.D.www.openhelix.com
Updated: Q1 2011
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ENCODE DCC at UCSC
ENCODE at UCSC: http://encodeproject.org
Introduction ENCODE Data Types Find and Use ENCODE Data ENCODE Downloads Additional ENCODE Topics Summary Exercises
ENCODE: www.genome.gov/10005107
ENCyclopedia of DNA Elements, NHGRI Consortium of international researchers UCSC is the Data Coordination Center
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ENCODE Background
Pilot phase, or phase I: www.genome.gov/26525202 Selected regions of the genome: 1%, 30 MB
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ENCODE Discoveries
“Marker” papers: Nature and issue of Genome Research Changes to our conceptual framework for the genome
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ENCODE Pilot Data and Beyond
ENCODE portal: http://genome.ucsc.edu/ENCODE/ Pilot ENCODE browser: genome.ucsc.edu/ENCODE/pilot.html
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ENCODE Next Phase: Production Phase
UCSC is the DCC for human and mouse data The portal is available: genome.ucsc.edu/ENCODE/ New aspects of the Production Phase projects
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ENCODE Production Phase Focus
ENCODE is now genome-wide Specific cell types and new technologies being applied Project focus topics selected, then supplemented
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chromatin
transcriptome/genes
promoters/regulatory sites
DNase sites
ENCODE Data is Flowing!
Data being submitted to UCSC DCC by data providers “Wranglers” ensure meta data is present Quality checks occur, data is released for use
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ENCODE DCC at UCSC
Copyright OpenHelix. No use or reproduction without express written consent 12
ENCODE at UCSC: http://encodeproject.org
Introduction ENCODE Data Types Find and Use ENCODE Data ENCODE Downloads Additional ENCODE Topics Summary Exercises
ENCODE Data Types Mapping data
Genes
Expression
Regulation
Variation
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ENCODE Tracks
identified with icon
Mapability Data
Mapability for unique regions Higher the peak, the more unique Cleavage intensity for structural profiling
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Broad: 36 mers
Duke: 20-35 mers
Rosetta: 35 mers
UMass: 15 mers more
uniquenot
unique
GENCODE http://www.sanger.ac.uk/PostGenomics/encode/
Gencode for assessment of protein coding genesCopyright OpenHelix. No use or reproduction without express written consent 15
Expression Data: RNA Localization
RNAs molecules, location in various cell types and fractionsCopyright OpenHelix. No use or reproduction without express written consent 16
http://en.wikipedia.org/wiki/MRNA
Expression Data: Presence of RNA or Exons
RNAs of various types Special look for long mRNAs and exons
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http://en.wikipedia.org/wiki/MRNA
Regulation Data
Regulation data Structure: modifications, open vs. closed chromatin
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Image from NIH
Regulation Data II
Transcription factor binding sites, TFBS RNA binding proteins
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TATA bound to DNA
Variation Data
Copy Number Variation (CNV) DataCopyright OpenHelix. No use or reproduction without express written consent 20
Super-Tracks
New strategies to integrate and display data Super-Tracks provide multiple data types to view See Track Description page for details, options, and keys
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ENCODE DCC at UCSC
Copyright OpenHelix. No use or reproduction without express written consent 22
ENCODE at UCSC: http://encodeproject.org
Introduction ENCODE Data Types Find and Use ENCODE Data ENCODE Downloads Additional ENCODE Topics Summary Exercises
General Organization
Tracks identified with icon Also available in Table Browser Description pages have options, settings, filters,
display keys, meta data, and referencesCopyright OpenHelix. No use or reproduction without express written consent 23
Configurationchoices, options,
filters
Display key,techniques,references,
contacts
click
ENCODE Data Policy genome.ucsc.edu/ENCODE/terms.html
Non-scoop window “Ft. Lauderdale agreement”
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Awareness of Embargo Dates
Track description pages, Table Browser interface Download pages
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ChIP-seq Data for TFBS
Yale TFBS Sample display near TP53 in “dense” visibility mode Chip-seq graphic adapted from: wikipedia.org/wiki/ChIP-on-chip
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TP53
stronger signalscell types + antibodies
Description Page, Upper
See description page for more display options Choose tracks and view styles
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display mode
peak configure
download
Description Page, Lower
Display conventions explained Methods and references
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ENCODE DCC at UCSC
Copyright OpenHelix. No use or reproduction without express written consent 29
ENCODE at UCSC: http://encodeproject.org
Introduction ENCODE Data Types Find and Use ENCODE Data ENCODE Downloads Additional ENCODE Topics Summary Exercises
Downloads and Release Log
Release log for a handy list of available data Download is offered; FTP recommended
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Release log
Human
Mouse
ENCODE DCC at UCSC
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ENCODE at UCSC: http://encodeproject.org
Introduction ENCODE Data Types Find and Use ENCODE Data ENCODE Downloads Additional ENCODE Topics Summary Exercises
New Features
Mouse data Proteomics data Publications Questions? UCSC mailing list, or ENCODE at NHGRI
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encode-announce mailing list:https://lists.soe.ucsc.edu/mailman/listinfo/encode-announce
UCSC Genome Browser discussion list:http://genome.ucsc.edu/contacts.html
modENCODE: modencode.org
A separate modENCODE: www.genome.gov/26524507 C. elegans and D. melanogaster modENCODE DCC: www.modencode.org
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Science 24 December 2010: Vol. 330
new
February 2011 issue
ENCODE DCC at UCSC
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ENCODE at UCSC: http://encodeproject.org
Introduction ENCODE Data Types Find and Use ENCODE Data ENCODE Downloads Additional ENCODE Topics Summary Exercises
Summary
Encyclopedia of DNA Elements Data Coordination Center at UCSC Genome Browser
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ENCODE DCC at UCSC
Copyright OpenHelix. No use or reproduction without express written consent 36
ENCODE at UCSC: http://encodeproject.org
Introduction ENCODE Data Types Find and Use ENCODE Data ENCODE Downloads Additional ENCODE Topics Summary Exercises
Copyright OpenHelix. No use or reproduction without express written consent 37
Hands-on session for ENCODE at UCSC
Exercises on the handouts We will walk through them together 2 styles: questions only, and step-by-step When we are finished the formal exercises, we can
help you to investigate issues that you want to understand for your research
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Notice:
The materials and slides offered are for non-commercial use only. Reproduction, distribution and/or use for commercial purposes is strictly prohibited.
Copyright 2010, OpenHelix, LLC
http://www.openhelix.com/ENCODE
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