1. Pathway Visualization
Sri Chaparala and Ansuman Chattopadhyay
Molecular Biology Information Service
Health Sciences Library System

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

3. ePath3D

4. 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: /mbc.E

5. https://goo.gl/cNWuaN

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

7. 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

8. 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  jsp.
Cytoscape This can be downloaded from  installed on Windows, Mac OS X, and Linux computers.

9. Cytoscape - publications
Links for publications: – Biological Network exploration with Cytoscape 3 – Must Read (this paper includes the datasets for gene expression data and how to load network …etc) 4 Gene-disease network analysis using Cytoscape Schizophrenia interactome with 504 novel protein-protein interactions

10. 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.

11. Cytoscape – A visualization Tool

12. Cytoscape

13. 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

14. Biological Interaction Networks
Nodes – Genes, proteins or other molecules
Edges – evidence from interaction

15. Cytoscape - Apps

16. 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.

17. Import data from public databases

18. Import data from Public databases Step 1 : Select Tool

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

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

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

22. Import data from Public databases Multiple gene Network

23. Import data from Public databases Multiple gene Network from Biogrid

24. Import pathway from public database - wikipathways

25. Import pathway from public database – wikipathways

26. Import pathway from public database – wikipathways

27. Import pathway from public database – wikipathways

28. Import pathway from public database – wikipathways - ERK pathway in Huntington disease

29. 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

30. RNA-seq Study

32. NCBI SRA
Untreated Vs DEX

33. 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

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

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

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

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

38. Dex vs Untreated gene Network Step 4: Network

39. Dex vs Untreated gene Network Step 4 : Save

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

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

42. Dex vs Untreated- DE gene Network

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

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

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

46. Dex vs Untreated gene Network - GO

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

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

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

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

51. Create the network manually – add nodes and edges

52. Create the network manually – add nodes and edges

53. Create the network manually – add nodes and edges

54. Create the network manually – add nodes and edges

55. Cytoscape - Help

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