- 27 lessons
- 0 quizzes
- 10 week duration
Overview
Module 1
Module 2
Module 3
Module 4
Module 5
Module 6
Module 7
Module 8
Module 9
RNASeq Pipeline using edgeR
Practice
Practice
Within R, there are many packages to perform gene set enrichment analysis but, due to ease, we
will use Database for Annotation, Visualization, and Integrated Discovery (DAVID) [27]. Open
https://david.ncifcrf.gov/ in web browser and select functional annotation.
1. Copy and paste ids of over expressed transcripts in upload gene list box.
2. Select the identifier “ENSEMBL_TRANSCRIPT_ID” from drop down menu. Select “Gene list”
and submit the list.
3. Some of our transcript ids will not be mapped because they were specific to our experiment
hence in the next page click on “Continue to Submit the IDs That DAVID Could Map”
4. Clear all default selections in next page (Fig. 10) and in Gene Ontology select
GOTERM_BP_DIRECT, GOTERM_CC_- DIRECT, and GOTERM_CC_DIRECT. Similarly
select KEGG_PATHWAY in Pathways and click on Functional Annotation Chart button.
5. Results will open in a separate browser window (Fig. 11) and clicking on download file will open
a text file in web browser. We can copy and paste the data in a text editor or spreadsheet application
You may try performing gene set enrichment analysis for under expressed transcripts as well