Gene set analyses of genomic datasets Andreas Schlicker Jelle ten Hoeve Lodewyk Wessels.
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Transcript of Gene set analyses of genomic datasets Andreas Schlicker Jelle ten Hoeve Lodewyk Wessels.
Gene set analyses of genomic datasets
Andreas SchlickerJelle ten HoeveLodewyk Wessels
Scenario
You have a gene expression dataset containing data from normal colon and adenoma samples.
- Which pathways are differentially regulated between normal and CRC samples?
-Do products of significantly differently expressed genes have specific functions (Gene Ontology)?
-Is there a significant overlap with published expression signatures (mutations, response to treatment, ...)?
Overview
• Mapping probe sets to functional annotation
• Hypergeometric test (Fisher’s exact test)
• Gene Set Enrichment Analysis
• Global test
Mapping probe sets to functional annotation
Examples of functional annotation
• Pathway databases (e.g. KEGG, Pathway Interaction Database, ConsensusPathDB, www.pathguide.org/)
• Functional categories (e.g. Gene Ontology, FunCat)
• Enzyme Commission numbers, disease associations, protein domains, …
• Published gene signatures
Example KEGG pathway
http://www.genome.jp/kegg/kegg2.html
Gene Ontology
• Collection of three separate ontologies: biological process, molecular function, cellular component
• Organized in a graph structure,
i.e. each term (concept, category) can have several parents
Gene Ontology (II)
Gene Ontology (III)
• Annotations with GO terms are assigned an evidence code:
G protein alpha subunit; GO:0060158 activation of phospholipase C …; ISS
• Different categories of evidence codes: experimental, computational, Author/Curator statement, fully automatic (IEA)
Details at http://www.geneontology.org/GO.evidence.shtml
The true path ruleIf a gene product is annotated with term A, all annotations with ancestors of A must also be valid.
•Gene product annotated with this termIt can also be annotated with the term‘s ancestors
•Different gene products are usually not annotated on the same level of the hierarchy
Hands on Time
The hypergeometric test / Fisher’s exact test
Basics
• Enrichment test
• Analysis steps:1. Single gene test (e.g. t-test for finding differentially expressed genes)
2. Do list (step 1) and gene sets overlap significantly?
diff. Expressed not diff. expressed
in gene set
not in gene set
Example
• Microarray: 20000, MAPK: 100, diff. expressed: 200
Fisher‘s exact test p = 0.26
diff. Expressed
not diff. expressed
total
MAPK 2 98 100
not MAPK 198 19702 19900
total 200 19800 20000
Example
• Microarray: 20000, MAPK: 100, diff. expressed: 200
Fisher‘s exact test p = 0.0005
diff. Expressed
not diff. expressed
total
MAPK 6 94 100
not MAPK 194 19706 19900
total 200 19800 20000
Another Example
• Consider having data on treatment response and gene mutation for samples in a dataset
! Choose threshold for resistance/sensitivity
Resistant Sensitive total
Mutated
WT
total
Problem with this approach
• Null hypothesis: Genes in the gene set are randomly drawn Significant result means that genes in the gene set are more alike than
random genes
• Problem: Gene set has been selected such that the genes have something in common False positives
Hands on Time
PAGE: Parametric Analysis of Gene Set Enrichment
Basics
• For each gene set and each sample: – How different is the mean expression of all genes in a gene set from
the overall mean expression?
• Applied to full expression matrix– No need for selecting interesting genes (based on e.g. t-test)
Basics
Problem with this approach
• What happens if one part of the pathway is up-regulated and the another part is down-regulated?
Hands on Time
The global test
Basics
• Group test
• Can the genes in the gene set predict the response?
• What is needed?– Clinical variable e.g. normal vs. CRC
– Gene expression e.g. GSE8671
– Gene sets e.g. KEGG pathways
Interpretation
• Interpretation of significant test result (w.r.t. genes):
– Gene set is associated with clinical variable
– “On average“ the genes in the set are associated with the clinical variable
– Not every gene needs to be associated
Interpretation
Interpretation
• Interpretation of significant test result (w.r.t. samples):
– Expression profile in the gene set differs for different values of the clinical variable
– Samples with similar value (clinical variable) have relatively similar expression profiles
Interpretation