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

Part 3 Pathway and network analysis (GeneMANIA & InnateDB)

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

Paste the Human Ensembl Gene IDs here and click on “GO”. GeneMANIA Use to perform pathway and network analysis. http://www.genemania.org/ 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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 2011. R package version 0.10.0. I prepared these guidelines to facilitate the “Bioinformatics for biologists workshop”, 20 Nov 2015, UTHSC – San Antonio. http://oncinfo.org/Bioinformatics+for+biologist+workshop Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015