1. Genome Biology & Applied Bioinformatics Mehmet Tevfik DORAK, MD PhD
Gene Sets
Mehmet Tevfik DORAK, MD PhD

2. Schedule

3. How to Generate a Gene Set Gene Set Enrichment Analysis (GSEA)
Outline
How to Generate a Gene Set
(NOT the nearest genes)
Gene Set Enrichment Analysis (GSEA)
(DAVID, GSEA, WebGestalt, ToppGene, HumanMine)

4. Gene Set Enrichment Possibilities
Gene Ontology (GO Terms)
Transcription Factor Binding Motifs
miRNA targets
Belonging to a Defined Group
(Molecular Signatures)

5. DAVID Link: https://david.ncifcrf.gov/home.jsp
Nature Protocol paper:

6. DAVID
Link:

7. DAVID
Link:

8. DAVID Default options are selected. Explore other options.
Link:

9. DAVID You have done a pathway analysis.
Link:

10. GSEA
Link:

11. GSEA/MSigDB
Link:

12. GSEA/MSigDB
Link:

13. Gene Ontology
Link:

14. CTDbase
Link: (Set Analyzer)

15. WebGestalt Link: WebGestalt: http://bioinfo.vanderbilt.edu/webgestalt
PAPER:

16. iGsea4Gwas
Link:

17. HumanMine
Links:
HumanMine:
List Analysis:

18. HumanMine
Links:
HumanMine:
List Analysis:

19. iGsea4Gwas Links: iGsea4Gwas: http://gsea4gwas.psych.ac.cn
ADDITIONAL NOTE:
PAPER:

20. MAGENTA (MATLAB)
Link:

21. GSEA-SNP (R)
Link:

22. Key Points
- A gene set can be generated from a SNP list using the targets of each SNP’s effect
- A gene set can be subject to many different types of enrichment of overlap analyses
- Results of an enrichment (including pathway) analysis may help to gain insight into disease biology

23. … Looking forward …..

24. Course material: http://www.dorak.info/genbiol/course.html