Pathway Visualization Sri Chaparala and Ansuman Chattopadhyay Molecular Biology Information Service Health Sciences Library System srichaparala@pitt.edu ansuman@pitt.edu

Topics Create a publication quality figure using ePath3D Visualize protein-protein interactions data in the context of networks using Cytoscape

ePath3D http://www.epath3d.com/

Start with … Liao, H.-J., & Carpenter, G. (2007). Role of the Sec61 translocon in EGF receptor trafficking to the nucleus and gene expression. Molecular Biology of the Cell, 18(3), 1064–1072. doi:10.1091/mbc.E06-09-0802

https://goo.gl/cNWuaN

A Visualization tool for network analysis http://www.cytoscape.org/ Cytoscape A Visualization tool for network analysis http://www.cytoscape.org/

Cytoscape – A visualization Tool http://www.cytoscape.org/

Cytoscape - Introduction A free open-source software application for visualizing and analyzing networks. Developed in 2001 by Institute for systems biology (a non profit organization), Seattle, WA Create networks with objects ( ex:proteins) and connecting the relationships between them (ex: interactions). Once this basic network is created, various attributes such as shapes and colors can be added to the network Networks can then be analyzed in many different ways using "plugins". Ex: Bingo – Gene Ontology terms

Software requirements Java SE 6: The Java Runtime Environment (JRE) must be installed on your computer. You can download the newest version of Java for free at http://java.sun.com/javase/downloads/index. jsp. Cytoscape This can be downloaded from http://cytoscape.org and installed on Windows, Mac OS X, and Linux computers.

Cytoscape - publications Links for publications: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC403769/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4174321/#S22title – Biological Network exploration with Cytoscape 3 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.002028 4 Gene-disease network analysis using Cytoscape https://www.ncbi.nlm.nih.gov/pubmed/27336055 Schizophrenia interactome with 504 novel protein-protein interactions https://academic.oup.com/nar/article/46/D1/D649/4626770 The Reactome pathway Knowledge base

Cytoscape statistics Daily startups of Cytoscape worldwide continues to increase, exceeding 5000 per day in late 2017 (as compared to about 3800 per day in 2016).

Cytoscape user manual http://manual.cytoscape.org/en/stable/

Types of data Cytoscape is for complex network analysis and visualization Gene or protein interaction networks Disease Networks Pathway associations Drug interaction network Social Networks

Biological Interaction Networks Nodes – Genes, proteins or other molecules Edges – evidence from interaction http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020284

Cytoscape - Apps

Creating networks There are different ways of creating networks in Cytoscape: Import data from public databases such as Biogrid, Reactomedb…etc Create network for one or multiple genes Import network files and create the network Protein interaction network Create an empty network and manually adding nodes and edges.

Import data from public databases

Import data from Public databases Step 1 : Select Tool

Import data from Public databases Step 2 : Input single/multiple genes

Import data from Public databases Step 3 : import network from Biogrid for one gene

Import data from Public databases Step 4 : Egfr Network from Biogrid

Import data from Public databases Multiple gene Network

Import data from Public databases Multiple gene Network from Biogrid

Import pathway from public database - wikipathways

Import pathway from public database – wikipathways

Import pathway from public database – wikipathways

Import pathway from public database – wikipathways

Import pathway from public database – wikipathways

Import as Network – wikipathways

Import Network and table files Create the gene list of interest (txt) and search for protein interactions (PPI) for those genes using STRING database (db) https://string-db.org/ Export the PPI network from string db as tsv file Import this tsv file into cytoscape as Network Then create labels for list of candidate genes – node (node as candidate) Import the node file into cytoscape as table file. cytoscape - style – fill color – discrete mapping – give different color for candidates

Example dataset - RNASeq study http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099625

Example dataset - RNASeq study http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52778

https://string-db.org/ String db https://string-db.org/

String db - PPI

String db – PPI – export network as tsv

Import Network and table files Create the gene list of interest (txt) and search for protein interactions (PPI) for those genes using STRING database (db) https://string-db.org/ Export the PPI network from string db as tsv file Import this tsv file into cytoscape as Network Then create labels for list of candidate genes – node (node as candidate) Import the node file into cytoscape as table file. cytoscape - style – fill color – discrete mapping – give different color for candidates

Import Network and table files Step 1 : Select Tool for importing Network

Import Network and table files Step 2 : Select Tool for importing Table

Dex vs Untreated gene Network Step 3: Label and color the nodes

Dex vs Untreated gene Network Step 3: Label and color the nodes

Dex vs Untreated gene Network Step 4: Network

Dex vs Untreated gene Network Step 4 : Save

Dex vs Untreated gene Network Step 5 : Export as an image

Dex vs Untreated gene Network Step 5 : Export as an Image

Dex vs Untreated- DE gene Network

Dex vs Untreated DE gene Network Step 6 : Select GO tool and network

Dex vs Untreated gene Network Step 7 : select gene ontology tool

Dex vs Untreated gene Network Step 8: Enriched GO terms from the network

Dex vs Untreated gene Network - GO

Dex vs Untreated gene Network – GO term associations – from selected genes

Dex vs Untreated gene Network – GO term associations – from selected genes

Dex vs Untreated gene Network – GO term associations – from selected genes

Dex vs Untreated gene Network – GO term associations – from selected genes

https://reactome.org/ Pathways – Reactome Reactome is a free, open-source, curated and peer-reviewed pathway database https://reactome.org/

Reactome statistics

Pathways – Reactome FI plugin in Cytoscape

Pathways – Reactome FI plugin in Cytoscape

Pathway enrichment analysis To analyze enriched pathways – right click – Analyze pathway enrichment

Pathway enrichment analysis – cont..

Network – overlay drugs

Create the network manually – add nodes and edges

Create the network manually – add nodes and edges

Create the network manually – add nodes and edges

Create the network manually – add nodes and edges

Cytoscape - Help

THANKS! Any questions? You can find us at: srichaparala@pitt.edu ansuman@pitt.edu