Tutorial session 2 Network annotation Exploring PPI networks using Cytoscape EMBO Practical Course...
-
Upload
neal-jones -
Category
Documents
-
view
220 -
download
5
Transcript of Tutorial session 2 Network annotation Exploring PPI networks using Cytoscape EMBO Practical Course...
Tutorial session 2Network annotation
Exploring PPI networks using Cytoscape
EMBO Practical Course Session 8
Nadezhda Doncheva and Piet Molenaar
Overview
Focus: Network annotation and visualization Loading and manipulating attributes
Identifier mapping
Mapping data onto the network
Use visuals to convey data
Concepts Vizmapper
Data Human Neuroblastoma mutated genes list
04/20/232
Attributes Nodes and edges can
have attributes associated with them Gene expression data Mass spectrometry data Protein structure
information Gene Ontology terms,
etc.
Cytoscape supports multiple data types: Numbers, Text, Logical, Lists...
04/20/233
Loading attributes Use pre-formatted attribute files Import attribute from table
Excel file
Comma or tab delimited text
Import attribute from web services NCBI Entrez Gene
Ensembl Biomart
Use ‘import attribute or expression matrix’ Create attributes manually in the attribute
browser04/20/234
Loading attributes from table (Demo)
04/20/235
Use Case 2.1: Neuroblastoma Childhood neuro endocrine tumor Young children Variable clinical outcome
Low stages Good prognosis
Numeric changes of chromosomal copy numbers
High stages Poor prognosis
Structural chromosomal defects (LOH1p / 11q etc)
Few gene defects identified MYCN amplification (20%) ALK activation (7%) CCND1 / PHOX2B / NF1
Use Case 2.1: Neuroblastoma Poor prognosis Subgroup (~1/3) characterized by MYCN
amplification Rest unknown
Use case: Assignment 2.1 Whole genome sequence of 86 tumor vs blood 1043 genes with mutations
1.Load the list of genes (neuroblastoma_mutated_symbols.txt) as a network
2.Use the tab separated dataset (neuroblastoma_mutated_annotations.txt) to map additional information
1. Make sure the attributes have informative names
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Import Attribute Table Files
04/20/238
Assignment 2.1 results1. Load the list; use
the same importer
1. No interactions yet
2. Load the annotations
1. Check text import settings
2. Check mapping settings
04/20/239
Attribute management
04/20/2310
Select attributes for display
Specific Attribute Tabs: for Nodes, Edges, and NetworkNode or Edge ID
Different type of attributes: Strings, Numbers, …
Tips & Tricks: Root Graph and sessions ”There is one graph to rule them all...” The networks in Cytoscape are all ”views” on
a single graph. Changing the attribute for a node in one
network will also change that attribute for a node with the same ID in all other loaded networks
There is no way to ”copy” a node and keep the same ID
Make a copy of the session
04/20/2311
Identifier mapping Identifiers (IDs) are ideally unique, stable name or
numbers But: too many IDs and different database records for
Gene, DNA, RNA, Protein The ID Mapping challenge:
Avoid errors by mapping IDs correctly Gene names are ambiguous Excel introduces errors Problems reaching 100 % coverage
Recommendations (for proteins and genes): Map everything to Entrez Gene IDs using a spreadsheet Manually curate missing mappings to achieve 100 %
coverage Be careful of Excel auto conversions
04/20/2312
Identifier mapping (Demo)
04/20/2313
Use case: Assignment 2.21. Use the Biomart plugin to map UniProt
identifiers on the genes
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Node Name Mapping
04/20/2314
Assignment 2.2 results Use the Ensemble 68
set Input data type is
HGNC symbols Import more than
just the UniProt IDs
04/20/2315
Data mapping
Mapping of data values associated with graph elements onto graph visuals
04/20/2316
Data mapping Visual attributes
Node fill color, border color, border width, size, shape, opacity, label
Edge type, color, width, ending type, ending size, ending color
Mapping types Passthrough (labels)
Continuous (numeric values)
Discrete (categories)
Visual style
04/20/2317
VizMapper
04/20/2318
Default Visual Style editor
List of Data attributes
List of Visual Styles
List of Visual attributes
Mapping definition
Data mapping (Demo)
04/20/2319
Tips & Tricks: Data mapping
Avoid cluttering your visualization with too much data
Map the data you are specifically interested in to call out meaningful differences
Mapping too much data to visual attributes may just confuse the viewer
Create multiple networks and map different values
04/20/2320
Use case: Assignment 2.31. Map the size of the nodes to the number of
occurrences
2. Map color to the tumor ids
1. Hint: use a rainbow pattern
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Visual Styles
04/20/2321
Assignment 2.3 results Use gradient
Readily shows higher number of mutations
Use rainbow Similar names, similar
colors
04/20/2322
Assignment 2.3 results
04/20/2323
Exploring expression data VistaClara plugin
Exploratory data analysis of multi-experiment microarray studies
A graphical and interactive alternative to the standard attribute browser
04/20/2324
VistaClara (Demo)
04/20/2325
Filtering & editing data Use filters
QuickFind nodes and edges
Index the network based on a node or edge attribute
Dynamic filtering for numerical attributes
Build complex filters using AND, OR, NOT relations
Define topological filters (considers properties of near-by nodes)
Create subnetworks
04/20/2326
Filtering & editing data (Demo)
04/20/2327
Use case: Assignment 2.41. What is the gene with most mutations?
2. Filter the network for genes with more than one mutation (why?) and save the new network.
3. Use the Bisogenet plugin...
1. ...to find interactions among these
2. ...to find interactions among these and their first neighbours (or explore different settings of Bisogenet according to your taste)
4. Store your session for later use
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Finding and Filtering Nodes and Edges
http://bio.cigb.edu.cu/biso/BisoGenet_User_Manual.pdf
04/20/2328
Assignment 2.4 results1. MYCN
1. Frequently amplified; no additional information
2. More likely not to be bystander
04/20/2329
Assignment 2.4 results1. MYCN
1. Frequently amplified; no additional information
2. More likely not to be bystander
3. Bisogenet
1. Between: Only large genes
2. Neighbours: Promising hairball
04/20/2330
To be continued…
Build, visualize and analyze your own network with Cytoscape Network generation Network annotation and visualization Network analysis
Identify active subnetworks
Analyze Gene Ontology enrichment
Perform topological analysis
Find network clusters
Find network motifs
04/20/2331