ENCODE Data Available through The UCSC Genome Browser

Transcription

1 ENCODE Data Available through The UCSC Genome Browser Osvaldo Graña CNIO Bioinformatics Unit Materials prepared by Mary Mangan, Ph.D. Warren C. Lathe, Ph.D. Version 3 1

2 ENCODE DCC at UCSC n Introduction n ENCODE Data Types n Find and Use ENCODE Data n ENCODE Downloads n Additional ENCODE Topics n Exercises ENCODE at UCSC: Copyright OpenHelix. No use or reproduction without express written consent 2

3 ENCODE: n ENCyclopedia of DNA Elements, NHGRI n Consortium of international researchers n UCSC is the Data Coordination Center 3

4 ENCODE Background n Pilot phase, or phase I: n Selected regions of the genome: 1%, 30 MB 4

5 ENCODE Discoveries n Marker papers: Nature and issue of Genome Research n Changes to our conceptual framework for the genome 5

6 ENCODE Pilot Data and Beyond n ENCODE portal: n Pilot ENCODE browser: genome.ucsc.edu/encode/pilot.html 6

7 ENCODE Next Phase: Production Phase n UCSC is the DCC for human and mouse data n The portal is available: genome.ucsc.edu/encode/ n New aspects of the Production Phase projects 7

8 ENCODE Production Phase Focus chromatin transcriptome/ genes promoters/ regulatory sites DNase sites n ENCODE is now genome-wide n Specific cell types and new technologies being applied 8

9 ENCODE Data is Flowing! n n n Data being submitted to UCSC DCC by data providers Wranglers ensure meta data is present Quality checks occur, data is released for use 9

10 ENCODE DCC at UCSC n Introduction n ENCODE Data Types n Find and Use ENCODE Data n ENCODE Downloads n Additional ENCODE Topics n Exercises ENCODE at UCSC: 10

11 ENCODE Data Types n Mapping data n Genes ENCODE Tracks identified with icon n Expression n Regulation n Variation 11

12 Mapability Data Broad: 36 mers Duke: mers Rosetta: 35 mers UMass: 15 mers not more unique unique n Mapability for unique regions n Higher the peak, the more unique n Cleavage intensity for structural profiling 12

13 GENCODE n Gencode for assessment of protein coding genes 13

14 Expression Data: RNA Localization n RNAs molecules, location in various cell types and fractions 14

15 Expression Data: Presence of RNA or Exons n RNAs of various types n Special look for long mrnas and exons 15

16 Regulation Data Image from NIH n Regulation data n Structure: modifications, open vs. closed chromatin 16

17 Regulation Data II TATA bound to DNA n Transcription factor binding sites, TFBS n RNA binding proteins 17

18 Variation Data n Copy Number Variation (CNV) Data 18

19 Super-Tracks n n n New strategies to integrate and display data Super-Tracks provide multiple data types to view See Track Description page for details, options, and keys 19

20 ENCODE DCC at UCSC n Introduction n ENCODE Data Types n Find and Use ENCODE Data n ENCODE Downloads n Additional ENCODE Topics n Exercises ENCODE at UCSC: 20

21 General Organization Configuration choices, options, filters click n n n Tracks identified with icon Also available in Table Browser Description pages have options, settings, filters, display keys, meta data, and references Display key, techniques, references, contacts 21

22 ENCODE Data Policy genome.ucsc.edu/encode/terms.html n Non-scoop window n Ft. Lauderdale agreement 22

23 Awareness of Embargo Dates n Track description pages, Table Browser interface n Download pages 23

24 ChIP-seq Data for TFBS TP53 cell types + antibodies stronger signals n Yale TFBS n Sample display near TP53 in dense visibility mode n Chip-seq graphic adapted from: wikipedia.org/wiki/chip-on-chip 24

25 Description Page, Upper display mode peak configure download n n See description page for more display options Choose tracks and view styles 25

26 Description Page, Lower n n Display conventions explained Methods and references 26

27 ENCODE DCC at UCSC n Introduction n ENCODE Data Types n Find and Use ENCODE Data n ENCODE Downloads n Additional ENCODE Topics n Exercises ENCODE at UCSC: 27

28 ENCODE specific section, downloads

29 ENCODE DCC at UCSC n Introduction n ENCODE Data Types n Find and Use ENCODE Data n ENCODE Downloads n Additional ENCODE Topics n Exercises ENCODE at UCSC: 29

30 New Features encode-announce mailing list: UCSC Genome Browser discussion list: n Mouse data n Proteomics data n Publications n Questions? UCSC mailing list, or ENCODE at NHGRI 30

31 modencode: modencode.org new February 2011 issue Science 24 December 2010: Vol. 330 n n n A separate modencode: C. elegans and D. melanogaster modencode DCC: 31

32 ENCODE DCC at UCSC n Introduction n ENCODE Data Types n Find and Use ENCODE Data n ENCODE Downloads n Additional ENCODE Topics n Exercises ENCODE at UCSC: Copyright OpenHelix. No use or reproduction without express written consent 32

33 Notice: n The materials and slides offered are for non-commercial use only. Reproduction, distribution and/or use for commercial purposes is strictly prohibited. n Copyright 2010, OpenHelix, LLC n Copyright OpenHelix. No use or reproduction without express written consent 33