Week10 DataVisualization Final · 2020-04-03 · 1 _____ Fall, 2017 GCBA/MGCB/BMI 815 Tools and Algorithms in Bioinformatics GCBA815/MCGB815/BMI815, Fall 2017 Week 10: Biological

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__________________________________________________________________________________________________Fall, 2017 GCBA/MGCB/BMI 815

Tools and Algorithms in BioinformaticsGCBA815/MCGB815/BMI815, Fall 2017

Week 10: Biological Data Visualization

Jasjit Banwait, Ph.D.Bioinformatics Data Analyst (Guda Lab)

Department of Genetics, Cell Biology and Anatomy

University of Nebraska Medical Center


1. Introduction to Biological Data Visualization

2. Data Visualization Tools

1. Cytoscape – Biological Network Visualization Tool

2. Circos - Genome-wide Circular plot

Outline

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Data Deluge


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5 V’s of Biological Data

Biological data has:VarietyVariabilityVolumeNeed VeracityNeed Visualization

Schultze, Joachim. (2015). Teaching 'big data' analysis to young immunologists. Nature immunology. 16. 902-5. 10.1038/ni.3250.


• Makes the data accessible

• Utilizes the computational power to understand the global picture

• Enables insight

• Enables integrative research

• Communicates

Why Visualization is Important?

Adopted from: Alexender Lex, Havard School of Engineering and Applied Sciences

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http://selection.datavisualization.ch/


• Cytoscape is a platform for visualizing molecular interaction

networks and biological pathways

• Allows integrating networks with annotations, gene expression

profiles and other attribute data

• Open-source platform

• Current version is 3.5.1

• http://www.cytoscape.org/

Introduction to Network Visualization with Cytoscape

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• Network is a mathematical structure composed of points

connected by lines

• Networks can be undirected or directed, depending on whether

the interaction between two neighboring nodes proceeds in both

directions or in only one of them, respectively.

Networks

Network GraphNodes Vertices (points)

Links Edges (Lines)


• A network can be connected (presented by a single component)

or disconnected (presented by several disjoint components)

• Networks having no cycles are termed trees. The more cycles the

network has, the more complex it is.

Networks as Graphs

connected disconnected

trees

cyclic graphs

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Path

Stars

Cycles

Complete Graphs

Bipartite Graphs

Basic Types of Networks


Air Transportation Network

https://flowingdata.com/2016/05/31/air-transportation-network/

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Social Network

http://smartblogs.com/wp-content/uploads/2014/03/social-network1.jpg


Infection Spread Risk Network

Gomes MFC, Pastore y Piontti A, Rossi L, Chao D, Longini I, Halloran ME, Vespignani A. Assessing the International Spreading Risk Associated with the 2014 West African Ebola Outbreak. PLOS Currents Outbreaks. 2014 Sep 2 . Edition 1. doi: 10.1371/currents.outbreaks.cd818f63d40e24aef769dda7df9e0da5.

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• Systems biology approach

• Represents molecular entities

• Represents interactions

• Data types

• Pathways/reactions

• Interaction networks

Network Biology


• Nodes: genes or other molecules

• Edges: interaction – can contain weights, directions

Biological Interaction Networks

Magtanong et al. 2011 Nature

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• Intra Cellular Networks

• Protein interaction networks

• Metabolic Networks

• Signaling Networks

• Gene Regulatory Networks

• Disease Networks

• Inter Cellular Networks

• Organ and Tissue Networks

• Ecological Networks

• Evolution Networks

Biological Networks


• It is increasingly recognized that complex systems cannot be

described in a reductionist view.

• Understanding the behavior of such systems starts with

understanding the topology of the corresponding network.

• Topological information is fundamental in constructing realistic

models for the function of the network.

Why Study Networks?

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The Protein Network of Drosophila

K.G. Guruharsha, et.al, A Protein Complex Network of Drosophila melanogaster, In Cell, Volume 147, Issue 3, 2011, Pages 690-703, ISSN 0092-8674,


• Which interactions and groups of interactions are likely to have

equivalent functions across species?

• Based on these similarities, can we predict new functional

information about proteins and interactions that are poorly

characterized?

• What do these relationships tell us about the evolution of proteins,

networks and whole species?

Importance of Networks in Biology

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1. Go to http://www.cytoscape.org/2. Click on “Download 3.5.1”3. On the downloads page, pick the appropriate version of the Cytoscape

based on the operating system configuration 4. For this class, we will be downloading Cytoscape 3.5.1 for Windows (32-

bit). Note: This is not recommended version. If you have access to a 64-bit machine, download the 64-bit version of the latest Cytoscape software for smooth and faster data visualization.

5. This version requires Java 8 to be installed on your machine. 6. Once the download completes, install the software by double-clicking the

downloaded file. 7. After installation finishes, open the Cytoscape software from the start

menu.

Downloading Cytoscape

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Welcome Screen


User Interface

Networkmanagementpanel Mainnetworkviewwindow

Attributebrowserpanel

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Control Panel

The Network tab of the Control Panel lists the available networks by name and provides information on the number of nodes and edges

The Style interface exists as a tab in the Control Panel and is divided into 3 tabs, for Node, Edge and Network properties.


• Go to File -> Save to save the session

1. Save Session

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2.1 Load Data: Import from Public Databases


2.2 Load Data: Import from Public Databases

2. Choose databases

3. Click Import

1. Enter Search Conditions and Click Search

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2.3 Load Data: Import Result


• Data sources

• Literature

• Search in other databases not listed in Cytoscape

• Own experiment (e.g., correlation between genes)

• Famous formats

• SIF

• A table

Alternate Ways to Load DataImport from Files

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Building & Storing Interaction Network

Source TargetA BA CA DC DD B

Network Input File or EdgeList FileA

B D

C

A

B D

C


• Interactor A <space or tab> Interaction_Type <space or tab> InteractorB

SIF File Format

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• From excel files or tab-delimited text tables

Load Data: Import from File


Load Data: Import from File

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Load Attributes: Import Table from File

The node and edge attributes can be imported as a table in Cytoscape.

As Node Attributes


• Go to File -> Save to save the session before we modify the

networks.

3. Save Session

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4.1 Go to the “Uniprot” Network.

4.2 Search “TP53” in the search box on top on the network window.

4.3 This will select the node representing TP53 gene.

4. Get a Subnetwork

Search a node by typing the gene name here

The selected/searched node, if present in the network, will be highlighted in the network as a yellow node and the table panel will provide the information regarding the selected node.


4.4 Now, select first neighbors of the selected node from the top menu

bar

Hide unselected nodes. This will overwrite the existing big network.

4.5 Create a subnetwork using the option in the menu bar.

4. Get a Subnetwork

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4.6 Resulting Subnetwork


4.7.1 Rename the sub network as “TP53_Network” by right clicking

the sub network name in the control panel and select Rename

Network option.

4.7.2 Type in the name for the network as “TP53_Network”.

4.7 Rename Network

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• A network layout is a process that positions the nodes and edges for the network.

• There are a large variety of layouts in Cytoscape and plugins might add new layouts.

• All of the layouts will appear under the Layouts menu.

Layouts

Grid Layout


5.1 Go to File->layouts and change the layout of the subnetwork as “organic”

• Try other layouts and see which layout fits well with the network. • Circular• Prefuse force directed

5. Change the Layout of the Subnetwork

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6. Removing Duplicate Edges and Self Loops

Resulting Network after removing self loops and duplicate edges


• In the control panel, select “Style” tab. You can remove previous

styles by clicking on the drop down arrow next to the applied style.

7. Change Style of the TP53 Network

Open and modify

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Change the Style

Node color

Each column represents some information that we have (this is a

column in the node table data)

Discrete: set a value for each type of information


7.1 Change the node color to “Green” in the TP53 network

7.2 Change the node shape to “ellipse”

7.3 Select “Lock node width and height”

7.4 In the edge tab, change the edge color to “red”.

7. Change the Style

All previous mappings won’t be removed automatically when you remove the style. While customizing the style of the network, make sure the previous settings are removed by clicking on the “Delete” icon next to the style.

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Resulting Network in Organic Layout


To save the network as a high quality image:

8. Saving a Visualization

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• Cytoscape has many tools called ‘Apps’

• Install by going to Apps -> App Manager

• Applications support

• Advanced analysis

• Biological analysis

• Integrating data

• Import special data

Apps in Cytoscape


Tutorial: 1. http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape32. Select “Basic Expression Analysis in Cytoscape 3” under

Cytoscape 3 User Tutorials. 3. Finish the tutorial up to “Observe the Network” Step.

Dataset1. http://wiki.cytoscape.org/Presentations/04_Expression_Data2. Download two data files

1. galFiltered.sif2. galExpData.pval (same as “galExpData.csv” in the

tutorial)

Cytoscape Tutorial Resource

While uploading the “galExpData.pval” file in the Cytoscape: Click on Advanced Options and delimit the data with “Space”. If your data has a header, make sure the “Use first line as column names” is Checked. Click “OK”.

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• Powerful data visualization tool in the form of circular layout by Krzywinski, M. et. al.

• Circos Software can be accessed from: http://circos.ca/• It is an ideal tool for visualization of genomic data, although other data can

also be used.

Circos


• Linear Layout has limitations

Circos (Examples)

http://www.nature.com/nrc/journal/v13/n7/full/nrc3537.html

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Circos (Examples)

Circos website



Circos (Examples)

Circos website

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• Works on a single configuration file• Karyotype file

• Backbone of the Circos image• Chromosome and its length/location (Optional: band)• Format: chr – LABEL ID START END COLOR• The first two fields are always “chr” and “-”

• Data Track file• Provides meaning to the backbone ideogram• association/characteristics of different data points• Links, tiles, histogram, scatterplot, highlight, connector, and text

• Other Configurations• Defines how karyotype and data track would be presented in the

Circos image.

How Does Circos Work?


ClicO FS – interactive web-based service of Circos

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1. Go to http://codoncloud.com:3000/home

2. Click on Demo tab

Tutorial

Typeinthenameoftheproject.Let’ssay“ClassDemo”

EnterCaptcha

Clickon“StartaDemoProject”


• Select both Human and Mouse Karyotype for the demo.

1. Select Karyotype

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2. Other Configurations/Settings

Repeat the color settings on Human Karyotype and proceed to next step.Keep moving further until you reach Data Tracks window.


3. Data Tracks

Proceed to the next step. You can change the data track settings. We are using the default settings for the demo.

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4. Output

• Click on “Output” tab to visualize the Circos diagram


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• Complex Circos figures can be created using multiple

configuration files, where each configuration file defines the

different layer, style, or figure type such as heatmap, box plot, etc.

• Learn more Circos at http://goo.gl/oeeKBw

(full link: http://circos.ca/documentation/tutorials)

Circos

Documents

Week10 DataVisualization Final · 2020-04-03 · 1 _____ Fall, 2017 GCBA/MGCB/BMI 815 Tools and Algorithms in Bioinformatics GCBA815/MCGB815/BMI815, Fall 2017 Week 10: Biological