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. Cytoscape – A visualization Tool

8. 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

9. 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.

10. Cytoscape - publications
Links for publications: – Biological Network exploration with Cytoscape Gene-disease network analysis using Cytoscape Schizophrenia interactome with 504 novel protein-protein interactions The Reactome pathway Knowledge base

11. 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).

12. Cytoscape user manual

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

29. Import as Network – wikipathways

30. 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)
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

31. Example dataset - RNASeq study

32. Example dataset - RNASeq study

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

34. String db - PPI

35. String db – PPI – export network as tsv

36. 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)
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

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

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

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

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

41. Dex vs Untreated gene Network Step 4: Network

42. Dex vs Untreated gene Network Step 4 : Save

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

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

45. Dex vs Untreated- DE gene Network

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

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

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

49. Dex vs Untreated gene Network - GO

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

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

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

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

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

55. Reactome statistics

56. Pathways – Reactome FI plugin in Cytoscape

57. Pathways – Reactome FI plugin in Cytoscape

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

59. Pathway enrichment analysis – cont..

60. Network – overlay drugs

61. Create the network manually – add nodes and edges

62. Create the network manually – add nodes and edges

63. Create the network manually – add nodes and edges

64. Create the network manually – add nodes and edges

65. Cytoscape - Help

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