Pathway Analysis

Overview

In this lab, we'll look at how to identify enriched biological pathways using enrichR.  For this analysis, we'll be using the differential analysis results we generated using DESeq.

Introduction

WHAT ARE PATHWAYS?

Biological pathways  are a series of molecular interactions that cause a change in the cell, produce a certain chemical product or emit a certain signal. Because these interactions are guided by the genes involved, biological pathways consist of series of genes that interact towards a certain biological outcome in the cell.  Biological pathways are categorized in multiple  databases, with kegg, biocarta, reactome being some of the most popular ones.

Pathway enrichment is a way of summarizing the FUNCTIONS AND TYPES of genes that are differentially expressed. 

CLASSICAL PATHWAY ENRICHMENT- OVER-REPRESENTATION ANALYSIS

Input: 

• A. Number of genes of interest, that is, in our DEG list (DEG).
  
  
• B. Total number of genes in the pathway
• C. Number of genes from our genes of interest (DEG) that are also in the pathway.

Enrichment test:  whether “DEG list” (A)  contain more representatives of a certain pathway than expected by chance  (Fisher’s exact, hypergeometric, or similar test).

If the number of genes from our list that belong to the glycolysis pathway ( C) is significant compared to the total number of genes in that pathway (B) and the total number of genes in the DEG list (B) , we consider that pathway to be enriched in our data.

WHAT DOES THIS MEAN TO US?

Many genes may be changing, but they may all be linked to similar biological processes. From a list of changing genes -> list of affected biologial processes.  We can better elucidate the biological events that are represented by our differential gene finding.

We also reduce the dataset considerably- from large number of genes to a smaller number of functions/processes. 

We go from up and down regulated genes between two conditions to up and down regulated processes between two conditions.

TOOLS AVAILABLE FOR GO/PATHWAY ENRICHMENT

Web-based tool for GO/pathway enrichment: Enrichr  

Let's run this web based tool by simply uploading our DEG list. These DEGs must be hugo gene names to be recognized.