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Lecture12 Functional Pathway Analysis

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Lecture12 Functional Pathway Analysis

Uploaded by

194140.mls21.ochs
Copyright
© © All Rights Reserved
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
You are on page 1/ 13

Lecture 12:

Functional/pathway analysis
“In the age of genomics, bioinformatics is not just a tool; it’s
a necessity”

Mr. Nabras Al-Mahrami


[email protected]

1
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.

• It involves associating these elements with specific biological processes,


molecular functions, or cellular components, often using ontological
frameworks like Gene Ontology (GO).

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).

3
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:

Pathway Type Definition Example

Chains of reactions converting


Glycolysis
Metabolic Pathways molecules into energy or building
(breaks down glucose for energy).
blocks.

Control gene expression by


Gene Regulation Pathways activating or repressing p53 Signaling Pathway
transcription and translation.

Relay signals from the cell surface MAPK pathway


Signal Transduction Pathways
to trigger cellular responses. (controls cell growth and division).

4
Introduction into Functional and Pathway Analysis

5
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

Summarize Summarize biological processes or other aspects of gene function

Perform Perform differential analysis – what pathways are different between samples?

Find Find a controller for a process (TF, miRNA)

Find Find new pathways or new pathway members

Discover Discover new gene function

Find Find a drug

Correlate Correlate with a disease or phenotype (candidate gene prioritization)

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Early Functional /Pathway Analysis
• Manually annotate list of differentially expressed (DE) genes

• Extremely time-consuming, not systematic, user-dependent

• Group together genes with similar function

• Conclude functional categories with most DE genes important in disease/condition under study.

• BUT may not be the right conclusion

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Functional /Pathway Analysis

Gene-set Enrichment 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

Where can I get these gene-sets?

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Functional /Pathway Analysis

Network-based pathway analysis


Allows researchers to understand the complex
interactions between genes, proteins, and
pathways. These approaches leverage biological
networks to uncover key functional insights that
are not apparent in traditional pathway analysis
methods

Metabolic network
Protein interaction networks
Represent biological entities (genes, proteins,
metabolites) as nodes and their interactions as
edges.

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Glossary

20
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)

• Ontology: A formal system for describing knowledge Dictionary: term definitions


Gene Ontology is:
• Hierarchically Structured
Functional categories are organized in a hierarchy, forming interrelated sets with increasing levels of specificity.
(e.g., parent-child relationships).
• Controlled Vocabulary
Functional categories are standardized and defined by experts, ensuring consistent usage for gene annotation.
• For Gene Product Function Annotation
Gene products (e.g., proteins) are annotated using Gene Ontology functional categories, referred to as "terms."

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