1. Bioinformatics for biologists
Dr. Habil Zare, PhD
PI of Oncinfo Lab
Assistant Professor, Department of Computer Science Texas State University
Presented at University of Texas, Health Science Center – San Antonio
20 November 2015

2. Part 3
Pathway and network analysis (GeneMANIA & InnateDB)

3. Simple network analysis
There are plenty of web-based tools to perform network analysis on a set of differentially expressed genes including:
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

4. Paste the Human Ensembl Gene IDs here and click on “GO”.
GeneMANIA
Use to perform pathway and network analysis.
Paste the Human Ensembl Gene IDs here and click on “GO”.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

5. GeneMANIA Analyzing a set of 100-200 genes takes 1-2 minutes.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

6. Choosing the criteria for connections
Check only “Physical interactions”,
“Pathway”, and “Genetic interaction”.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

7. Excluding redundant genes
From View menu, click on “Rest layout”.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

8. Functional analysis Click on Functions.
Click on a process to color the corresponding nodes in the network accordingly.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

9. Investigating particular genes
Click on a gene..
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

10. Investigating particular genes
From the View menu, click on Highlight neighboours.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

11. Investigating particular genes
Click on Genes and then a specific gene to see its connections with other genes in the network.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

12. Click on Pathway Analysis and then Analysis
InnateDB
Use to perform pathway and network analysis.
Click on Pathway Analysis and then Analysis
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

13. Click on Pathway Analysis and then Analysis
InnateDB
Use to perform pathway and network analysis.
Click on Pathway Analysis and then Analysis
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

14. Uploading gene names to InnateDB
Click on Web Form.
Copy and paste the gene names in the window that opens.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

15. Uploading gene names to InnateDB
Choose Cross-reference ID
Choose Ensembl and click on OK.
Click on Column 1.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

16. Uploading gene names to InnateDB
Click on Next.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

17. Pathway over representation analysis (ORA)
Click on Pathway ORA.
Leave the defaults
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

18. Pathway over representation analysis (ORA)
You can choose the database.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

19. Pathway over representation analysis (ORA)
Click on
“Do a different analysis using the same uploaded data”.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

20. Network analysis using InnatDB
Choose Network Analysis.
If you do not filter the results, the indirect interactions will be make a larger network.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

21. Network analysis using InnatDB
Move the mouse pointer over a gene to highlight its interactions.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

22. InnateDB provide a few way of visualizing the network.
Visualizing networks
InnateDB provide a few way of visualizing the network.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

23. E.g., follow NetworkAnalyst
Visualizing networks
E.g., follow NetworkAnalyst
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

24. Visualizing using NetworkAnalys
You can obtain high-quality visualization suitable for publications.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

25. Visualizing using BioLayout
You can obtain high-quality visualization suitable for publications.
Bioinformatics for biologists workshop, Dr. Habil Zare, Oncinfo Lab UTHSC San Antonio, 20 Nov 2015

26. Acknowledgments (Oncinfo Lab Members)
Dr. Habil Zare, PhD
The PI
Computational Biologist
Dr. Amir Forpushani, PhD
Postdoc,
Rupesh Agrihari
Grad student,
Computer Science
I would like to thank Amir for helping me in preparing the network and pathway analysis slides, and Rupesh for his assistance to the audience during the workshop.

27. References:
DESeq2 manualhttps://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf
Huber W and Reyes A. pasilla: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down ,Genome Research R package version
I prepared these guidelines to facilitate the “Bioinformatics for biologists workshop”, Nov 2015, UTHSC – San Antonio.
Instaling BioLinux using VM, Dr. Habil Zare Oct 2015