MetaCore data analysis suite and functional analysis Ying-Fan Chen, Ph. D. Feb. 5, 2010.

MetaCore data analysis suite and MetaCore data analysis suite and functional analysisfunctional analysis

Ying-Fan Chen, Ph. D.Ying-Fan Chen, Ph. D.

Feb. 5, 2010Feb. 5, 2010

Outline Introduction

由成大生資中心進入：使用前設定以及注意事項

簡介使用方法

試用帳號實際操作

Upload Data Analyze Data 快速 workflow

MapEditor

“Knowledge-based” functional data analysis

HTS, HCS

Cancer relevant annotations, datatabases,

Active cpds analysis screening

• Knowledge Base:

- protein interactions

- causative associations (gene-disease, cpd-disease)

- pathways, protein complexes

- ontologies

Experimental data depository

Data parsing, normalization

Data analysis tools: EA, networks, interactome

Biomarkers TargetsCompound scoring

一般 Array Data 分析流程

Differentially expressed genes, proteins (normalization, QC)

Analysis:Networks, pathways,

Statistics on functional categories

Prioritized gene listsGenes are functionally connected

“Cut off” setting ( eg, log ratio; fold change)

eg, GeneSpring GX

eg, MetaCore

Functional analysis tools

Enrichment analysis for gene, protein, compound sets– Hyper G, GSEA, GSA etc.– Multidimensional analysis: multiple ontologies

• GO processes• GG processes• Canonical pathways• Diseases

– Export of sub-sets for network analysis– Low resolution

1000 genes; Multiple sets

Network analysis– Multiple pre-filters (species, interactions mechanisms,

organelles etc.)

– Parameters: enrichment with genes from set,

canonical pathways, specific protein classes

– Algorithms: SP, DI, AN, TFs, Receptors etc.

– Statistics: hubs, preferred pathways etc.

– Highest resolution: individual proteins or isoforms

Interactome analysis– Whole-set analysis

– Over- and underconnected nodes in the dataset

• Interactions neighborhood

• TFs, kinases, receptors, etc.

– Scoring for interactions within set: FDR

ResolutionExperiment filters – Species, orthologs, localizations, tissues etc.– Custom list of targets, IDs

“Most important” genes

- Highly connected TFs, receptors, etc.-Hubs from important networks-Highest expressed/mutated genes

Agilent Affymetrix Proteomic SAGE

Concurrent visualization of different data types, experiments

OutlineIntroduction


簡介使用方法



MapEditor

http://www.binfo.ncku.edu.tw/2010_genomics/

使用者電腦設定

OutlineIntroduction


簡介使用方法



MapEditor

上傳成功！

early s phase list

http://training.genego.com/

http://training.genego.com/

1. 上傳檔案藍色資料夾2. 下載 gene list

OutlineIntroduction


簡介使用方法



MapEditor

Analysis data

分析前注意事項

Remove data from Exp. File to yourself file

GS875

Active Data

Analysis data

GeneGo Pathway Maps

http://portal.genego.com/cgi/exp_stat.cgi?diagram_type=maps&ez_page=1

http://portal.genego.com/cgi/exp_stat.cgi?diagram_type=maps&ez_page=1

如何找出這些 genes list?

往下拉！

12 genes

Analysis data

GeneGo Diseases (by Biomarkers)

http://portal.genego.com/cgi/exp_stat.cgi?diagram_type=dis&ez_page=1

http://portal.genego.com/cgi/exp_stat.cgi?diagram_type=dis&ez_page=1

Analysis data demo2

OutlineIntroduction


簡介使用方法



MapEditor

請一直按著 Ctrll 鍵

workflow

OutlineIntroduction


簡介使用方法



MapEditor

Save

Publish Map…

OutlineIntroduction


簡介使用方法



MapEditor

MetaCore data analysis suite and functional analysis Ying-Fan Chen, Ph. D. Feb. 5, 2010.

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Transcript of MetaCore data analysis suite and functional analysis Ying-Fan Chen, Ph. D. Feb. 5, 2010.