Lecture12 Functional Pathway Analysis
Lecture12 Functional Pathway Analysis
Functional/pathway analysis
“In the age of genomics, bioinformatics is not just a tool; it’s
a necessity”
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Lecture
The objective of the Lecture
• Explain what functional and pathway analysis is.
• Highlight methods of functional and pathway analysis .
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Introduction into Functional and Pathway Analysis
Functional Analysis
• Refers to the process of determining the biological roles, activities, or functions
of genes, proteins, or other biomolecules.
An ontological framework is a structured system used to organize, categorize, and describe knowledge in a specific domain
• Hierarchy:
• Terms are connected by relationships such as:
Is-a: A specific term is a subtype of a broader category (e.g., apoptosis is-a biological process).
Part-of: A specific term contributes to a larger process (e.g., "cytoplasmic translation" is part-of protein biosynthesis).
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Introduction into Functional and Pathway Analysis
Pathway Analysis
• It is the study of predefined networks of biological interactions (pathways) to understand the roles and relationships
of genes, proteins, or metabolites within these networks.
• Major Types:
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Introduction into Functional and Pathway Analysis
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Functional /Pathway Analysis
What is it?
A method to identify classes of genes or proteins that are overrepresented in a large set of genes or proteins,
and may have an association with disease phenotypes.
Over-representation: the representation of a group in a category that exceeds our expectations for that group, or differs substantially
from the representation of others in that category
Primary data for this analysis is commonly sourced from gene expression arrays …
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What do you want to accomplish with your gene list?
Action Description
Perform Perform differential analysis – what pathways are different between samples?
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Early Functional /Pathway Analysis
• Manually annotate list of differentially expressed (DE) genes
• Conclude functional categories with most DE genes important in disease/condition under study.
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Functional /Pathway Analysis
1. Break down cellular function into gene sets and every set of genes is associated to a specific cellular function,
process, component or pathway.
2. Which gene-sets summarize at best gene expression patterns
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Functional /Pathway Analysis
Metabolic network
Protein interaction networks
Represent biological entities (genes, proteins,
metabolites) as nodes and their interactions as
edges.
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Glossary
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What is the Gene Ontology (GO)?
• Major bioinformatics initiative to unify the representation of gene and gene product attributes
across all species.
• Set of biological phrases (terms) which are applied to genes (e.g. protein kinase, apoptosis,
membrane)