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

2. Schedule

3. Outline ENTREZ GENE / UNIPROT Gene x Protein x Disease Connections
(HumanMine, Disease Connect, CoreMine, ToppGene)
Gene Co-expression
Gene Co-regulation
Cytoscape

4. ENTREZ GENE
Link:

5. UNIPROT
Link:

6. EMBL-EBI
Link:

7. EMBL-EBI
Link:
Search template:

8. STRING
Link:

9. STRING
Link:

10. STRING
Link:

11. EXPRESSION & CO-EXPRESSION
Link:
Select the link on the following page for correlation analysis

12. EXPRESSION & CO-EXPRESSION
Co-expression analysis results for ERG:

13. CO-REGULATION Links: CORD: http://cord-db.org
Paper:

14. GIANT
Link:

15. Protein x Protein Interaction: PPI Finder
Link: /

16. Protein x Protein Interaction: PPI Finder
Link:

17. Gene x Protein x Disease Connections
HumanMine,
Disease Connect,
CoreMine, ToppGene
For links, see:

18. Gene x Environment Interactions
Link:

19. CYTOSCAPE Links: http://www.cytoscape.org
Reference paper (2003):

20. Key Points
- Gene x gene, and protein x protein interactions can easily be explored using existing resources.
- Besides interactions, co-expression and co-regulation of genes can also be explored using user friendly web interfaces which bring together a massive amount of data for this purpose.
- Cytoscape is the ultimate tool for visualizing molecular interaction networks using raw data. Cytoscape is not a web tool, and should be run on your own computer.

21. … Looking forward …..

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