Bioinformatics Lec2

Volcano Plots

• Show which genes are significantly differentially expressed in a condition

Direct functions

Actual biological pathways of a gene

Indirect functions

Larger scale impacts of the pathway a gene is involved in

Genes can be associated into a set based on ____ or _____

pathway involvement, similarity

What is a gene set?

A priori defined set of genes

______, ______, and ______, are sources of gene sets

Literature and experimental evidence, curated databases, computational predictions

Gene ontologies are _____ with _______relationships

gene sets; hierarchal relationships

Three aspects of gene ontology

• Biological processes

• Molecular function

• Cellular component

The GO structure is ____ due to many __________ relationships

acyclic, parent-child

Molecular function

• Catalytic/enzymatic “activity”

Cellular component

• Structural components/complexes

Biological Processes

Pathways (ie. exocytosis)

What is the motivation for gene set analysis?

Is my hitlist enriched in any function?

Differences between gene set analysis compared to individual gene analysis

• Genes analyzed as sets

• Individual genes don’t need to be significantly differentially expressed

• Gene sets must be enriched for the finding to be statistically significant

Over-representation analysis (ORA) takes a list of ______ genes and sees if any gene sets are _______

significant; overrepresented

Pro of ORA

Easy to understand and run

Cons of ORA

• Does not account for genes that are borderline on the p-value cutoff

• Possible that no genes are significant to begin with

GSEA step 1

Rank ALL genes from high-low expression in one condition

GSEA step 2

• Identify individual genes within the data set and ranked list

• Black lines indicate genes that are present in the gene set of question

• Determine if there is enrichment

A positive enrichment score indicates

Upregulated genes in X pathway are enriched

A negative enrichment score indicates

Downregulated genes in X pathway are enriched.

Problems with ontology and enrichment

• Ontologies are incomplete (based on experimental evidence and statistics)

• Ontologies are always changing