Content Comparison

...

GO terms provide a standardized vocabulary to describe genes and gene products from different species. GO terms allow us to assign functionality to genes. The following properties are described for gene products:

• cellular component, describes where in a cell a gene acts, what cellular unit the gene is part of

• molecular function, describes the function carried out by the gene, such as binding or catalysis;

• biological process,  a set of molecular functions, with a defined beginning and end, makes up a biological process. This describes biological phenomenon like DNA replication.

All GO terms have an ID that looks like GO:0006260 and a name like DNA replication. 

...

GO terms are hierarchical consisting of broader parent GO terms and narrower child GO terms. For example, DNA replication is a child of GO term:cellular metabolic process. DNA replication has child GO terms like regulation of DNA replication, strand elongation.

WHAT IS GO ENRICHMENT?Image RemovedImage Removed

...

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

CLASSICAL GO ENRICHMENT

Input: 

• A. Total number of genes we are looking at (ALL genes).

• B. Number of genes of interest, that is, in our DEG list (DEG).
  

• C. Total number of genes in the GO term

• D. Number of genes from our genes of interest (DEG) that are also in the GO term.

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

...

Web-based tool for GO/pathway enrichment: Enrichr  

Run Gorilla- Classical enrichment

...

...

Get the data for running gorilla

#Make sure you are in the right location
 
cds
cd my_rnaseq_course/day_4_partA/go_enrichment

...

Get all input files from DESeq2 output:

"","id","baseMean","baseMeanA","baseMeanB","foldChange","log2FoldChange","pval","padj"

"131","FBgn0000370",7637.91654540105,4217.77033402576,11058.0627567763,2.62177925326286,1.39054621964443,1.2887282997047e-116,7.22484613473489e-113

"2489","FBgn0025682",6038.35042952997,3300.21617337019,8776.48468568974,2.65936660649935,1.41108267336748,1.36704751839828e-116,7.22484613473489e-113

......

INPUT FILE 1: DEG (contains the 76 genes that meet our fold change an p value cut offs)

FBgn0000370

FBgn0025682

FBgn0086904

...

...

Pull out all the gene ids corresponding to DEGs

#Alter this old command to pull out Gene ids corresponding to DEGs and store it in a file called DEG
sed 's/,/\t/g' deseq2_htseq_C1_vs_C2.csv|awk '{if ((($3>=1)||($3<=-1))&&($6<=0.05)) print $1}' |sed 's/"//g'|grep '^FB' > DEG

.....

INPUT FILE 2: ALL (contains all 14869 genes)

FBgn0000370

FBgn0025682

FBgn0086904

.....

...

Pull out all the gene ids

#Command to pull out ALL gene ids and store it in a file called ALL
sed 's/,/\t/g' deseq2_htseq_C1_vs_C2.csv|cut -f 1|sed 's/"//g'|grep '^FB' > ALL

...

SCP THE DATA OVER TO YOUR COMPUTER:

scp

#ON ls6: copy the path for the ALL and DEG files
pwd
 
#ON LOCAL COMPUTER: from a terminal tab 
scp <username>@ls6.tacc.utexas.edu:<pathtofileson/DEG> .
scp <username>@ls6.tacc.utexas.edu:<pathtofileson/ALL> .

RUN GORILLA USING THE UNRANKED METHOD: http://cbl-gorilla.cs.technion.ac.il/

Run Gorilla- Rank based enrichment

INPUT FILE: ALLRANKED (all genes, ranked by adjusted pvalue)

 FBgn0000370

 FBgn0025682

 FBgn0086904

...

...

Pull out all the gene ids, ranked by pvalue

##Command to pull out ALL gene ids, sorted by adjpvalue store it in a file called ALLRANKED
#Remember we already sorted our results by adjusted pvalue in the deseq2 script before writing it out to a file. So #you just need to pull out the gene ids in the order it already is in. 
sed 's/,/\t/g' deseq2_htseq_C1_vs_C2.csv|cut -f 1|sed 's/"//g'|grep '^FB' > ALLRANKED

SCP THE DATA OVER TO YOUR COMPUTER:

scp

#ON ls6: copy the path for the ALLRANKED file
pwd
 
#ON LOCAL COMPUTER: from a terminal tab 
scp <username>@ls6.tacc.utexas.edu:<pathtofileson/ALLRANKED> .

RUN GORILLA USING THE RANKED METHOD: http://cbl-gorilla.cs.technion.ac.il/

Go back to COURSE OUTLINE