SlideShare uses cookies to improve functionality and performance, and to provide you with relevant advertising. If you continue browsing the site, you agree to the use of cookies on this website. See our User Agreement and Privacy Policy.
SlideShare uses cookies to improve functionality and performance, and to provide you with relevant advertising. If you continue browsing the site, you agree to the use of cookies on this website. See our Privacy Policy and User Agreement for details.
Successfully reported this slideshow.
Activate your 14 day free trial to unlock unlimited reading.
Introduction to Biological Network Analysis and Visualization with Cytoscape Part1
Introduction to Biological Network Analysis and Visualization with Cytoscape Part1
1.
Introduction to Biological Network
Analysis and Visualization with
Cytoscape
Keiichiro Ono
Cytoscape Core Developer Team
UC, San Diego Trey Ideker Lab / National Resource for Network Biology
5/10/2016 The Scripps Research Institute
Lecture 1: Basics
2.
Keiichiro Ono
Cytoscape Core Developer
since 2005
@UCSD Trey Ideker Lab
Area of Interest:
Biological Data Integration &
Visualization
3.
Agenda
• Lecture 1 (Today):
Introduction to Biological Network
Analysis and Visualization
• What is the benefits of biological
network analysis and visualization?
• Introduction to Cytoscape
• Preview of Lecture 2: cyREST
• Lecture 2:
Reproducible Analysis & Visualization
• Introduction to Jupyter Notebook
• Create a reproducible network
visualization workflows with Python
4.
All documents, data, and code are available here:
https://github.com/idekerlab/tsri-lecture
16.
Networks Pathways
Collection of binary interactions Human-curated / detailed
Large Scale Small Scale
Generated from omics-data Constructed from literature
19.
Benefits of Network Analysis
- You have list of N genes from your
screening
- Now you want to know:
- Relationships among those
genes
- Functions
- etc.
Screening 1
PPARG
TCF7L2
RETN
IRS1
HNF1A
HNF4A
KCNJ11
GCK
LIPC
PTPN1
ABCC8
ENPP1
HNF1B
21.
Benefits of Network Analysis
- You can see the relationships among the group
of biological entities
- Find drag targets
- Overrepresented functions AND their
connections
22.
Gene List to Network to Biological Insight
- How?
- You need to search, integrate, and visualize
multiple data sources
This is what you will learn in this lecture
26.
Cytoscape
- Open Source (LGPL)
- Free for both commercial and academic use
- Developed and maintained by universities,
companies, and research institutions
- UC, San Diego
- University of Toronto
- UC, San Francisco
- ISB
- And collaborators world-wide
27.
Cytoscape
- De-facto standard software in biological network
research community
- Large User and Developer Community
- Expandable by Apps
- This is why Cytoscape is a Platform, not a
simple desktop application
28.
C. Elegans Interactome from BioGRID Database
?
29.
Biological Networks
- Tell us anything by themselves
- Just a big hairball…
37.
Network Data Analysis
Analysis
Graph Analysis
NetworkX
igraph
Cytoscape
Python
Pandas
NumPy
SciPy
Excel
Visualization
Desktop
Gephi
Cytoscape
matplotlib
Web
Cytoscape.js
sigma.js
d3
NDV3
d3.chart
Google Charts
Data Storage
Graph
Neo4j
GraphX
Document
MongoDB
Relational
MySQL
IPython
3rd Party Apps
NetworkAnalyzer
38.
Network Data Analysis
Analysis
Visualization
Desktop
Gephi
Cytoscape
matplotlib
Web
Cytoscape.js
sigma.js
d3
NDV3
d3.chart
Google Charts
Data Storage
48.
Creating Visualizations in Cytoscape
Name Type
BRCA1 gene
MAP2K1 gene
C05981 compound
• Mapping from Type to Node Shape
• Mapping from Type to Node Color
C05981
BRCA1
MAP2K1
Creating mappings from data points
to Visual Properties
49.
Network Data
Annotated
Networks
Attributes
Analyzed Data
51.
Cytoscape Apps
- Extension programs to
add new features to
Cytoscape
- formerly called Plugins
- Large App developer/
user community
- This is why Cytoscape
is so successful in life
science community!
53.
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
54.
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns
using the Reactome functional interaction network
60.
Overview of App Ecosystem
A travel guide to Cytoscape plugins
Rintaro Saito, Michael E Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-
Liang Wang, Samad Lotia, Alexander R Pico, Gary D Bader, Trey Ideker (2012)
Nature Methods 9 (11) p. 1069-1076
63.
Choose a Right Tool
Analysis VisualizationData Preparation
64.
Data Visualization Tools
http://selection.datavisualization.ch/
65.
Data Visualization Tools
http://selection.datavisualization.ch/
66.
Data Visualization Tools
http://selection.datavisualization.ch/
67.
Tools
• In some cases, you can get exact same result using different tools
• Example: Data preparation (cleansing / cleansing)
• But if you choose right tools, you can do it 100x faster than
others.
• ex: Re-formatting complex data sets
• Excel vs Python Script
• Some recommendations:
• R/Bioconductor, Python/Pandas, Git/GitHub/Gist
72.
- Goal: Help others to
understand your data
- Emphasize what you
want to tell
- Use color, shape,
size of objects
effectively!
- Excellent resource for
data visualization
- Tamara Munzner’s Web Site:
http://www.cs.ubc.ca/~tmm/
Data Visualization
76.
Design is complicated,
because humans are complicated.
Design is a process to avoid bad designs.
Mike Bostock (New York Times Visualization Team. Creator of D3.js)
77.
It is hard to generalize the design process, but we
can avoid pitfalls by following some basic rules.
78.
Every pixel should
carry information.
Edward Tufte
79.
Avoid Data Overload
• Mapping too many attributes makes your visualization
awful!
• It is hard to see the overall trend of your data sets if too
many channels are used in a image
96.
NCBI Gene ID 672
On Chromosome 17
GO Terms
DNA Repair
Cell Cycle
DNA Binding
Ensemble ID
ENSG00000012048
BRCA1
97.
Data Tables for Cytoscape
- Example:
- Numeric
- Gene expression profiles
- Network statistics calculated in other
applications, such as R
- Confidence scores for edges
- Text (or categorical)
- GO annotation for genes
- List of genes related to disease X
- Targets for FDA approved drugs
- Genes on KEGG Pathway Y
- Clusters / group / community calculated
in external programs
- …
98.
Your Data Sets
- Anything saved as a table can be
loaded into Cytoscape
- Excel
- Tab Delimited Document
- CSV
- As long as proper mapping key is
available, Cytoscape can map them to
your networks.
99.
Mapping Key in
the Network
Mapping Key
in the Table
109.
Visual Style
- Collection of mappings from
Attributes to Visual
Properties
110.
Visual Styles
- Defaults + Mappings
- Expression values to node color
- Gene function to node shape
- Interaction detection method to edge line
type
- Confidence score to edge width
112.
Data Controls The View
• Photoshop / Illustrator
• You control the pixels and objects on the display
• Data Visualization Tools (including Cytoscape)
• Data points are mapped to visual properties
• Color
• Size
130.
Further Readings
• My presentation slides
• http://www.slideshare.net/keiono
• This deck of will be uploaded today
131.
Further Readings 1
- Introduction to Network Biology
- Deciphering Protein–Protein Interactions. Part I. Experimental
Techniques and Databases
Shoemaker BA, Panchenko AR (2007) Deciphering Protein–Protein
Interactions. Part I. Experimental Techniques and Databases. PLoS
Comput Biol 3(3): e42.doi:10.1371/journal.pcbi.0030042
- Deciphering Protein–Protein Interactions. Part II. Computational
Methods to Predict Protein and Domain Interaction Partners
Shoemaker BA, Panchenko AR (2007) Deciphering Protein–Protein
Interactions. Part II. Computational Methods to Predict Protein and
Domain Interaction Partners. PLoS Comput Biol 3(4): e43. doi:10.1371/
journal.pcbi.0030043
132.
Further Readings 2
- Overview of Cytoscape Apps (Plugins)
- A travel guide to Cytoscape plugins
Rintaro Saito, Michael E Smoot, Keiichiro Ono, Johannes Ruscheinski,
Peng-Liang Wang, Samad Lotia, Alexander R Pico, Gary D Bader, Trey
Ideker (2012) Nature Methods 9 (11) p. 1069-1076
- Sample Protocol (based on 2.x)
− Integration of biological networks and gene expression data using
Cytoscape
Cline, et al. Nature Protocols, 2, 2366-2382 (2007).
133.
Further Readings 3
- Cytoscape Tutorial Booklet:
Analysis and Visualization of Biological Networks with Cytoscape
- http://www.rbvi.ucsf.edu/Outreach/Workshops/ISMBTutorial.pdf