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![Biology
Chemistry
Biochemical Enrichment Analysis
Informatics
Pathway over representation
analysis (ORA)
Steps:
1. Use MBrole to conduct:
• Pathway over representation analysis
• url: http://csbg.cnb.csic.es/mbrole/
ORA:
• is used to evaluate whether a particular set of
metabolites is represented more than expected by
chance within a given compound list
[doi: 10.1093/nar/gkq329].
• p-value is calculated using hypergeometric or
Fisher’s exact test](https://image.slidesharecdn.com/6-metaboliteenrichmentanalysis-140217114156-phpapp02/75/6-metabolite-enrichment-analysis-4-2048.jpg)
![Biology
Chemistry
Biochemical Enrichment Analysis
Informatics
MetaboAnalyst:
Pathway Enrichment Analysis
(PEA)
Use MetaboAnalyst to conduct:
• Pathway enrichment Analysis
• url: http://www.metaboanalyst.ca/MetaboAnalyst/faces/UploadView.jsp
PEA:
• is an advanced form of over representation analysis (ORA) which takes
into account pathway topology and is based on gene set enrichment
analysis (GSEA) [doi:10.1093/bioinformatics/btq418]
• p-value is calculated using hypergeometric or Fisher’s exact test
Questions:
1. What pathway is the most important based on ORA and topology?](https://image.slidesharecdn.com/6-metaboliteenrichmentanalysis-140217114156-phpapp02/75/6-metabolite-enrichment-analysis-8-2048.jpg)
Uploaded byDmitry Grapov
6 metabolite enrichment analysis
This document discusses using various bioinformatics tools and databases to conduct pathway enrichment analysis on metabolite data from pumpkin and tomatillo leaves. It describes using the KEGG database to visualize pathways, MBRole to perform over-representation analysis using a hypergeometric test, and MetaboAnalyst to perform pathway enrichment analysis incorporating pathway topology. The goal is to identify significantly over-represented biological pathways and map metabolites of interest to pathways to understand biochemical differences between the plant leaves.
6 metabolite enrichment analysis
- 1. Biology Chemistry Biochemical Enrichment Analysis Informatics Identificationof altered biochemical domains between pumpkin and tomatillo leaf metabolites Goal: Identify significantly over represented biological pathways based on significant differences in leaf metabolites (Use DATA: Pathway Enrichment data.csv) Topics: 1. KEGG Database 2. MetaboAnalyst: Pathway enrichment analysis 3. MBrole: Over Representation Analysis 4. Hypergeometric test for enrichment
- 2. Biology KEGG Pathway Visualization Chemistry BiochemicalEnrichment Analysis Informatics Goals: Use KEGG to: 1. Overview glutamate entry in KEGG (C00025) 2. Visualize a pathway of interest 3. Map metabolite of interest to pathway • • http://www.kegg.jp/dbget-bin/www_bget?C00025 http://www.kegg.jp/keggbin/show_pathway?org_name=ath&mapno=00250 • Mapping example C00064 green, black C00025 green, black
- 3. Biology Pathway Visualization Chemistry Biochemical EnrichmentAnalysis Informatics
- 4. Biology Chemistry Biochemical Enrichment Analysis Informatics Pathwayover representation analysis (ORA) Steps: 1. Use MBrole to conduct: • Pathway over representation analysis • url: http://csbg.cnb.csic.es/mbrole/ ORA: • is used to evaluate whether a particular set of metabolites is represented more than expected by chance within a given compound list [doi: 10.1093/nar/gkq329]. • p-value is calculated using hypergeometric or Fisher’s exact test
- 5. Biology Chemistry Informatics MBRole: Pathway Over Representation Analysis(ORA) Biochemical Enrichment Analysis Goal: Identify an over represented pathway and visualize it in KEGG
- 6.
- 7. Biology Chemistry Test for significance: HypergeometricTest Biochemical Enrichment Analysis Informatics How to calculate statistics to determine network enrichment? hit.num = 51 # number of significantly changed pathway metabolites set.num = 1455 # number of metabolites in pathway full = 3358 # all possible metabolites in organism q.size = 72 # number of significantly changed metabolites phyper(hit.num-1, set.num, full-set.num, q.size, lower.tail=F) = 1.717553e-06
- 8. Biology Chemistry Biochemical Enrichment Analysis Informatics MetaboAnalyst: PathwayEnrichment Analysis (PEA) Use MetaboAnalyst to conduct: • Pathway enrichment Analysis • url: http://www.metaboanalyst.ca/MetaboAnalyst/faces/UploadView.jsp PEA: • is an advanced form of over representation analysis (ORA) which takes into account pathway topology and is based on gene set enrichment analysis (GSEA) [doi:10.1093/bioinformatics/btq418] • p-value is calculated using hypergeometric or Fisher’s exact test Questions: 1. What pathway is the most important based on ORA and topology?
- 9. Biology KEGG Pathway Enrichment Chemistry BiochemicalEnrichment Analysis Informatics