The 11th Japan-Korea-China Bioinformatic Training Course...

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_________________________ The 11th Japan-Korea-China Bioinformatic Training Course & Symposium _________________________ Soochow University, Suzhou, China June 17 – 18, 2013

Transcript of The 11th Japan-Korea-China Bioinformatic Training Course...

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_________________________The 11th Japan-Korea-China BioinformaticTraining Course & Symposium_________________________

Soochow University, Suzhou, ChinaJune 17 – 18, 2013

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< CKJ Bioinformatics Training Course 2013> 11th China-Korea-Japan

Bioinformatics Training CourseBig Data needs Big Idea:

What can we solve from genetic information?

Soochow University, Suzhou, China17 June, 2013

Takashi GojoboriCenter for Information Biology

National Institute of Genetics (NIG), Mishima, Japan

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Ion PGM

Ion Proton

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Item DescriptionRead Length and Speed 512 nanopores x 15bp/sec => ~7500 bp/sec

Read Accuracy 99.8%6 Hours Life Time 150 x 106bpApplied Currency /Blockage 60 picoamps to anywhere from 20-40 picoamps

No. of nanopore 2,000 nanopores / cartridge.Will become available in early 2013 containing over 8,000 nanopores.→Delivers a complete human genome in 15 minutes.

Sample Preparation Any user-derived sample preparation resulting in double stranded DNA (dsDNA) in solution is compatible with the system.

Amplification No sample amplification.Cost $900Commercialization Oxford Nanopore intends to commercialise GridION and MinION

directly to customers within 2012.

Nano Pore Oxford (2012)

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From the Genome Revolution to Sequencing Revolution

Sequencing =>/ Genome sequencing/ Meta-genomics/ Gene Expression

Transcription- EST, SAGE, and CAGE)/ miRNA, functional non-coding RNAs, siRNAs

(Translational regulation)/ CHIP-Seq (CHIP-Chip, CHIP-Pet)/ PPI (Two hybrid System)/ Epi-genomics (Methylated sites)

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- Problem -

•Sydney Brenner says,“Low input, High throughput, and No output”!

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Cells, Tissues,OrgansSpeciesPopula-

tions

Next-generationsequencers

Sequencedata

NGSBio-samples Database

Data AnalysisInformatics

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/Cells, /Tissues,/Organs/ Species

/Popula-tions+

/Time/Environ-

ments/Conditions

/Genome /Meta-

genome/Epi-genome

/RNA-seq/CHIP-seq

/PPI/Synthe-tic

NGS

Bio-samples DatabaseData AnalysisInformatics

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Hospitals and Clinical Stations(applied fields)

Basic Science andBiomedical Sciences

(Life Science Dept and Medical School at University)

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Hospitals and Clinical Stations(applied fields)

Basic Science andBiomedical Sciences

(Life Science Dept and Medical School at University)

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Issues on retrieving the necessary informationLack of the standard format without unified information often hinders research and development seriously

DBDB

Medicine

How about the relations between each information?

Where is the information needed?

DB DB

LabExperiment

DB

Too many databases….

Protein Structure

User

Journals

?

DB

Sequencedata

?

?

(The Gist)

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“Submission only” DatabaseTraditional Model

Be Unified and Easily Retrievable Format from Sporadic Information !

“Unified and Easy Retrievable” Database

New Model

Which one to use?

?

This is a right one to use!

Databases with various formats

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D. Howe, M. Costanzo, P. Fey, T. Gojobori, L. Hannick, W. Hide, D. Hill, R. Kania, M. Schaeffer,

S. St Pierre, S. Tweigger, and S. Rhee Nature (2008) 455: 47-50

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We conducted Japanese Governmental projects.

I. FANTOM1~5 Project (1999~)sponsored by RIKEN/DDBJ with MEXT (Ministry of Education, Science, Sports, and Culture).

II. H-Invitational Human Transcripts Project (2000~)sponsored by METI (Ministry of Economy, Trade, and Industry) and JBiC.

III. Human Genome Network Project (2004~2009)sponsored byMEXT.

IV. Cell Innovation Project (2009~2014)sponsored by MEXT .

IV. Structural Life Science Project (2012~2017)sponsored by MEXT .

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For mouse full-length cDNAs,Nature (2001) 409:685-690Nature (2002) 420: 563-573Science (2005) 309: 1559-1563Nature Genetics (2009) 41: 553-62

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Co-organized by JBIRC and DDBJAttended by more than 118 people from 40 organizations such as

JBIRC, DDBJ, NCBI, EBI, Swiss-Prot/SIB, SangerInstitute, NCI-MGC, DOE, NIH, DKFZ, CNHGC(Shanghai), RIKEN, Tokyo U, MIPS, CNRS, MCW, TIGR, CBRC, Murdoch U, U Iowa, Karolinska Int., WashU, U Cincinnati,

Tokyo MD U, KRIBB, South African Bioinfor Inst, U College London, Reverse Proteomics Res. Inst., Kazusa DNA Inst, Weizmann Inst, Royal Inst. Tech. Sweden, Penn State U, Osaka U, Keio U, Kyushu U, TIT, Ludwig Inst.

Brazil, Kyoto U, German Can.Inst., and NIGSupported by

JBIC, METI, MEXT, CRNS, NIH, and DOE

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H-Inv

NIH

DKFZ

Tokyo U・NEDO

Kazusa

Helix Inst.

Shanghai

41, 118 FLcDNA clones21, 037 Loci (possible genes)5, 155 New loci vs RefSeq.

Nature (2002) 419: 3-4 PLoS Biol (2004) 2: 1-21Science (2004) 304: 368

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Nature (2002) 419: 3-4 News

September 5, 2002

This will be a real human gene catalogue – not predicted from the human genome sequence…

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H-InvDB Annotation Summary (rel 8.0)

Functional Annotation Category Number*

protein coding 36,096I: Identical to known human protein (experimentally validated)

15,141

II: Similar to known protein 6,532

III: InterPro domain-containing protein 1,026

IV: Conserved hypothetical protein 1,744

V: Hypothetical protein 5,813

VI: Hypothetical short protein (20-80 aa) 5,840

VII: Pseudogene candidate (transcribed) 752

non-protein-coding 8,329

*representative transcriptsCategories I, II and III (known function) define a reliable set of human protein-coding genes (22,699 genes).

Current  number:~ 36,000.

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Distribution of tissue_type origin(H-InvDB_8.0 representative transcripts)

*Total 694 tissue_types for 27,819 transcripts.

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Statistics of human gene polymorphisms

SNP

5’UTR 3’UTR

41,369 95,496 * 85,423

Synonymous

Nonsynonymous40,484

53,754

1258**

1993 1474 4926

Total

8393

207,374

215,767 Total 43,369 96,970 90,349

Nonsense(Stop codon) Extension

75 **

Indel

ORF

Non- frameshifting 180Cause frameshift 12895’UTR-inORF 2 inORF-3’UTR 3

Termination Codon

Synonymous123

• dbSNP build 125, human genome assembly build 35 and H-InvDB release 3 (representative transcripts of protein-coding genes) were used.

• * includes 311 unclassified SNPs• ** allele that matches the cDNA sequence was considered to be ancestral

Yamaguchi-Kabata, et al. (2008)

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H-InvDB Advanced Search ToolSearch Conditions Advanced Search Main Window

Three sets of data in H-InvDB1. representative transcripts: 46,4992. representative alternative splicing variants: 61,4733. all transcripts: 296,912

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H-InvDB Enrichment Analysis Tool (HEAT)

Execution Button

HEAT is a data-mining tool for finding common features that is enriched in a given human gene set.

Annotation items analyzed:- Chromosomal band- Gene family/group- Gene Ontology (GO)- Functional domains (InterPro)- Structural domains (SCOP)- Metabolic pathways (KEGG)- Subcellular localization

(Wolf PSORT)- Tissue-specific gene expression

(H-ANGEL)- Sequence motifs in promoter

regions (JASPAR)

Knowledge discovery tool from H-InvDB

URL: http://hinv.jp/HEAT/

(Insert Gene List Here)

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Genome Network Project

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Human CAGE Tag 46,205,347Tags

PARK7

HTT

PARK2

PSEN1

APOE

PARK1 ALS1

ALS2

ALS4

PSEN2

APP

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An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder MCollaborators (594)

Nature (2012)489(7414):57-74.

Abstract

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

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Susumu Ohno(1928 – 2000)

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Junk DNA• Term coined in the article “So much ‘junk

DNA’ in our genome”

(Brookhaven Symposium on Biology, 1972)

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Cell Innovation Project (2009~2014)

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Cell Innovation Project (2009~2014)Data Analysis Center‐Gojobori’s Lab

Data Analysis Center

Sequencing Center

Unify management betweentwo centers・LSA Cooperation/Data Transfer・Joint research & development

Public

Co‐Research Institute

Strengthen cooperation with Co‐research Institute【e.g.】・Developing  Miyano lab. “CelliP”

Provide Information・starting up “Wiki”

NGS First Timer

NGS Experienced one

Above all things, Result!・Analysis(DAP)・Progress(DTM‐IF)・Reading(GE)

Want to analyze freely!・WKT

Want  some more advanced analysis!・Individual support【e.g.】・Miyano Lab. “CelliP”Technical  Researcher

Leading Research Project

Basic Research・NGS Public data research・Assemble research etc.

Activities Research/Investigation

Establish analysis flow・Bisulfite analysis etc.

Research individual life phenomena・Various collaborative research etc.

Integrate NGS data &knowledge, and spread them out globally

Develop Know‐how【e.g.】・Ito lab.  “Bisulfite”

Development

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NGS Data Analysis Software 

Class Tools 導入

公開

備考

マッピング

BWA ◯ ◯ CP

Bowtie ◯ ◯ CP

SOAP2 ◯ ◯ CP

FAMSR(Original)

◯ ◯ CP

MLA(Original)

◯ ◯ CP

Maq ◯

SeqMap ◯ ◯ P

BLAST+ ◯ ◯ P

mpiBLAST ◯

BLAT ◯

LAST ◯

BSMAP ◯ ◯ P

BFAST ◯

TopHat ◯ ◯ P

TopHat‐Fusion

MUMMER ◯

「◯:Done、△:Underway」 「C: CONG、P:Pipeline」 ■:2011 AdditionsClass Tools 導

入公開

備考

アセンブル

Velvet ◯ ◯ C

ABySS ◯

SOAPdenovo

◯ ◯ C

ALLPATH ◯

Hassp(独自)

◯ ◯ C

SSAHA2 ◯

PCAP ◯

IMAGE ◯

CLUSTALW ◯

RNA‐seq

rSeq ◯ ◯ CP

ERANGE ◯

Cufflinks ◯ ◯ P

RNA‐seq*denovo

Trans‐ABySS

Oases ◯

Trinity ◯

small‐rna

mireap ◯

Class Tools 公開

備考

ViennaRNA 

ChIP‐seq

ISOLATE

PeakSeq

MACS

QuEST

SISSRs ◯ C

FindPeaks

GPS

BS‐seq

Bismark ◯ P

rrbsmap

Exome

SOAPsnp

GATK

ANNOVAR ◯ P

Utility

FASTX‐Toolkit

◯ CP

SAMtools ◯ CP

Picard

EMBOSS

Class Tools 導入

公開

備考

dnaa ◯

BEDtools ◯ ◯ CP

FastQC ◯ ◯ P

NGS附属

Corona Lite

CASAVA ◯

BioScope ◯ △ P

Helisphere ◯

Newbler ◯

分担機関作成ツール

エピゲノム解析(宮野研)

Cellip(宮野研)

イメージアノテーション

解析(豊田研)

オミックス情報統合

解析(豊田研)

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Analysis Pipeline System• We developed a pipeline system which automatically run routine analysis

– This system provide rapid analyses by parallel processing with multiple servers.– Prevent unnecessary file copy and use the storage feature properly to meet the different needs

Cooperation Analysis Pipeline Utilizing Data Analysis 

Result yCloud 

Analysis yOrder‐made Analysis

Sharing Information

Classification Pipeline name Description

Mapping

BWA Program: Fast and enough reliable mapping with few InDel and mismatches

SOAP2 Mapping program: Very fast when the number of query is big. Start‐up cost is high.

Bowtie Mapping program: Very fast mapping without detecting InDel. Start‐up cost is low.

FAMSR Pipeline: Browse the result  of considering splice site by genome view

MLA Pipeline: Search mutation of insertion/deficiency and browse them by genome view

RNA‐seq rSeq Pipeline:  Calculate the expression of  known gene models by RPKM method

ChIP‐seqSISSRs ChIP‐Seq anal Pipeline:  Detect binding site and browse them by genome view

SISSRs: filtering Pipeline: Make list of specifig binding sites and directory link it to browser.*

BisulfiteBSMAP: Mapping Pipeline:  Identify methylated base and browse them by genome view*

BAMAP: Window anal Pipeline: Report highly methylated genomic regions.*

List of available pipeline*Under development(to be released in Oct.)

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Construction of ChIP‐seq Data Analysis Pipeline

For ChIP‐seq

• Sharing ChiP‐seq analysis work flow (Built into analysis pipeline)

Bowtie Map Results (SAM) SISSRs BS Results

(TSV)

WindowAnalysis

Report(HTML)

Data Base(PG SQL)

DBLoader

Sequence(FASTQ)

Base view of binding regionBinding region report

Cooperation Analysis Pipeline Utilizing Data Analysis 

Result yCloud 

Analysis yOrder‐made Analysis

Sharing Information

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Binding region judged by SISSRs

Sticking +strand lead

Sticking – strand lead

Hyper Link

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For Bisulfite

Construction of Bisulfite Data Analysis 

• Sharing Bisulfite analysis work flow (Built into analysis pipeline)

BSMAPGenome

Map Results (BSMAP)

Repeat Filter

Map Results(BSMAP)

Calc.Meth Rate 

Results(TSV)

WindowAnalysis

Report(HTML)

Data Base(PG SQL)

DBLoader

Sequence(FASTQ)

Ability to display methylated baseUtilizing Window and center data

Hyper Link

Cooperation Analysis Pipeline Utilizing Data Analysis 

Result yCloud 

Analysis yOrder‐made Analysis

Sharing Information

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T C T C A C A A G G T A C AT C T C A C A A G G T A C A

Methylated base 

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System to view analysis result• Developed the viewer to check the status of genome mapping 

– display multiple mapping result at high speed and in parallel

DEMOClick Here

Link to GNP web.

Base display function

Magnify

Base display feature for confirming deletion, insertion, substitution and methylated base

Cooperation Analysis Pipeline Utilizing Data Analysis 

Result yCloud 

Analysis yOrder‐made Analysis

Sharing Information 

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Utilization of KEISuper‐Computer

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Biological hierarchyEcosystem

|Population

|Individual

|Organ

|Tissue

|Cell

|Organella

|Bio-molecules

|Molecules

(Environments)

(Human population)

(Human)

(Lung, Stomach)

(Epidermal tissue)

(Red blood cell)

(Mitochondria)

(DNA, RNA, Proteins)

(H2O, O2)

Inte

grat

ion

Evolution

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Information ExplosionIn Life Science

Beyond the 4th Paradigm proposed by Jim Gray

・・・・・・・・・・・・・・・・2010                              2020                         2030                      2040

11!st Paradigm: Experiments

112nd Paradigm: Theory

113rd Paradigm: Simulation

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4th Paradigm:Data‐driven Scientific Discovery

5th Paradigm:Data‐driven Scientific Innovation

Jim Gray

・Info for global environments

・Info for genomes・ Info for outer space・ Info for oceans・ Info for the earth・・・・・

InformationExplosion

Scientific Innovation and its Application to the Society

Genome Information Society

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Acknowledgements/ Genome Network Project Consortium

- RIKEN (Hayashizaki’s group)- Tokyo U. (Sugano’s group)- Hitachi Co. Ltd.- Kieo U. (Yanagawa’s group)- Saitama Medical College (Okazaki’s group)

/ H-Invitational Consortium/ BIRC at AIST, Tokyo, Japan/ NIG – Genome Network Platform group

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Thank you!