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/

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 – Must Read (this paper includes the datasets for gene expression data and how to load network …etc) 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

Cytoscape statistics PubMed Cytoscape Citations as of Feb. 10, 2016 According to Google Scholar, Cytoscape is cited in nearly 145 papers per month. According to PubMed, Cytoscape is cited in nearly 70 papers per month. http://www.cytoscape.org/stat.html

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

Cytoscape

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 - ERK pathway in Huntington disease

Import Network and table files Get the list of genes (txt) and put them in string database and get the interactions for those genes or the interactions within those genes Then export the PPI from string in 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 txt file. Then in cytoscape go to style – fill color – discrete mapping – give different color for candidates

RNA-seq Study http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099625

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52778

NCBI SRA Untreated Vs DEX

Import Network and table files Get the list of genes (txt) and put them in string database and get the interactions for those genes or the interactions within those genes Then export the PPI from string in 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 txt file. Then in cytoscape go to 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

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