making sense of the encode project ( encyclopedia of dna elements) data
DESCRIPTION
Making Sense of the ENCODE Project ( ENCyclopedia Of DNA Elements) Data. Ansuman Chattopadhyay , PhD Head, Molecular Biology Information Services Health Sciences Library System University of Pittsburgh [email protected]. Topics. Introduction Gene Regulation Epigenetics ENCODE Project - PowerPoint PPT PresentationTRANSCRIPT
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Making Sense of the ENCODE Project (ENCyclopedia Of DNA Elements) Data
Ansuman Chattopadhyay, PhDHead, Molecular Biology Information ServicesHealth Sciences Library SystemUniversity of [email protected]
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Topics Introduction
Gene Regulation Epigenetics
ENCODE Project Plus and minuses
UCSC Encode Browser Noteworthy Tools
Regulome db, NCBI Epigenome Genboree
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Topics
retrieve promoter sequences
determine transcription factor occupancy
browse through the epigenetic biochemical markers
Histone modifications, DNA methylation etc., -predict the location of enhancers, silencers and promoters
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INTRODUCTION
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Genomic achievements since the Human Genome Project
http://www.hsls.pitt.edu/guides/genetics
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DNA Sequencing Cost
http://www.hsls.pitt.edu/molbio
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Progress in Genomics1990 2003 2013
Time
Technology
6-8 year 3-4 months 2-3 days Time
1B 10-50 M 4-6 K
Cost Source: Eric Green; HGP10 Symposium
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Genome Biology : Time Line
1976
RNA Bacteriophage MS2
2001
Human Genome Draft Seq
2003
Published Complete Human Ref Genome
2007
Diploid Genome seq ofan Individual Human
2011
Published Complete Genomes: 1863 organisms
1995
HaemophilusInfluenza
2008
Jim Watson Genome
Yeast
1996
1998
C. elegans
2002Drosophila
http://www.hsls.pitt.edu/molbio
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Big DATA Biology
Single GeneSingle Protein
Single lab
Small Science
Multi Gene – System Wide –
High throughputMulti Institution
Big Science
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ENCODE
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Epigenome andEncyclopedia of DNA
Elements Project
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ENCODE
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An excellent movie on transcription
http://www.hsls.pitt.edu/guides/genetics
http://vcell.ndsu.edu/animations/transcription/index.htm
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Promoter, Enhancer and Silencer
Source: http://www.cbs.dtu.dk/dtucourse/cookbooks/dave/Lekt03bkg.html
http://www.hsls.pitt.edu/guides/genetics
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Retrieve promoter sequence for a gene
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UCSC Genome Browserhttp://genome.ucsc.edu/cgi-bin/hgGateway
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Gene of Interest
EGFR BDNF
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Promoter Sequence
Generic Promoter Seq UCSC Genome Browser
Human Curated Promoter Seq Biobase TransPro CSH TRED Eukaryotic Promoter Database (EPD) Epigenome Data
http://www.hsls.pitt.edu/guides/genetics
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http://www.hsls.pitt.edu/molbio
Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/sequence.swfhttp://media.hsls.pitt.edu/media/clres2705/sequence_2.swf
ResourcesUCSC Genome Browser: http://genome.ucsc.edu/NCBI Entrez Gene: http://www.ncbi.nlm.nih.gov/gene
Find sequence information for a gene
-genomic -promoter - intron-exon coordinates-mRNA -protein
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Spatiotemporal gene expression
TP53
EGFR
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A movie on regulated transcription
http://vcell.ndsu.edu/animations/regulatedtranscription/index.htm
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Epigenetic mechanisms
Source: NCBIhttp://www.ncbi.nlm.nih.gov/books/NBK45788/#epi_sci_bkgrd.About_Epigenetics
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Chromatin Immuno-Precititation-Seq(ChIP-Seq)
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Epigenetic MarkersLandmark Paper:
http://www.nature.com/ng/journal/v39/n3/full/ng1966.html
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Histone Modifications
http://goo.gl/GQ9V8
http://www.hsls.pitt.edu/guides/genetics
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http://www.nature.com/encode/#/threads
http://www.nature.com/encode/#/threads
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ENCODE DATA 30 papers 1640 data sets - a matrix of Assay Vs Cell
Types
74.7% of the genome is transcribed, 56.1% is associated with modifed histones 15.2% is found in open-chromatin areas 8.5% binds transcription factors 4.6% consists of methylated CpG dinucleotides
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ENCODE Project
http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001046
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Encode Cell Types
http://genome.ucsc.edu/ENCODE/cellTypes.html
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UCSC ENCODE BROWSER
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EGFR and Sec61g
Role of the Sec61 translocon in EGF receptor trafficking to the nucleus and gene expression.Liao HJ, Carpenter G.Mol Biol Cell. 2007 Mar;18(3):1064-72. Epub 2007 Jan 10.
http://www.hsls.pitt.edu/guides/genetics
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Sec61g and EGFR
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http://www.hsls.pitt.edu/molbio
Link to the video tutorial:http://media.hsls.pitt.edu/media/molbiovideos/encode1-ac0212.swfhttp://media.hsls.pitt.edu/media/molbiovideos/encode2-ac0212.swfhttp://media.hsls.pitt.edu/media/molbiovideos/encode3-ac0212.swf
ResourceUCSC Genome Browser: http://genome.ucsc.edu/
Identify promoter, enhancer and silencer sequences by browsing the epigenomic markers generated by the ENCODE project
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Cell Lines
K562
NHLF
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UCSC browser link-genes: http://goo.gl/QVsvN
Video Tutorials Browse the region of human chromosome 7 part 1: http://media.hsls.pitt.edu/media/clres2705/ucsc_genes.swf
Browse the region of human chromosome 7 part 2: http://media.hsls.pitt.edu/media/clres2705/ucsc_snp.swf
NCBI Mapviewer: http://media.hsls.pitt.edu/media/clres2705/ncbimapviewer.swf
Place a mRNA or peptide sequence into the human genome: http://media.hsls.pitt.edu/media/clres2705/blat.swf
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ENCODE Criticisms
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Noteworthy Tools
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Regulome, Haploreg and Genebore
http://goo.gl/jhBvS
http://goo.gl/oP5gj
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Regulome
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HaploReg
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NCBI Roadmap Epigenomics Page
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Thank you!Any questions?
Ansuman [email protected] 412-648-1297
http://www.hsls.pitt.edu/guides/genetics