Pathway and Network Analysis Service

Cancer Stem Cell program

Veronique Voisin

veronique.voisin@gmail.com

located at TMDT 8th floor on Tuesday

Introduction about the service:

The Pathway and Network Analysis Service is freely available to all Cancer Stem Cell program members. High-throughput genomic experiments (e.g. gene expression, protein expression, molecular interactions, large-scale genetic screens and other omics data) lead to the identification of large gene lists. The interpretation of results and the formulation of consistent biological hypotheses from these gene lists are challenging. Computational approaches can aid interpretation by relating the gene lists to knowledge about the biological system. To help researchers interpret their results, we are developing a new consulting and analysis service for pathway and network analysis. Analysis will be conducted in close collaboration with researchers on each project (Cancer Stem Cell research program) to ensure correct input data and effective interpretation of results.

Information about Pathway and Network Analysis

Suggested readings:
- GSEA
  - Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50.
    http://www.ncbi.nlm.nih.gov/pubmed/16199517
- Enrichment Map:
  - Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. Merico D, Isserlin R, Stueker O, Emili A, Bader GD. PLoS One. 2010 Nov 15;5(11):e13984.
    http://www.ncbi.nlm.nih.gov/pubmed/21085593
What you can expect:

How to use the service

who can use the service
how to book an appointment
data input requirement

Service SOP

Standard input requirements

calendar

the pathway and analysis calendar: https://www.google.com/calendar/embed?src=vvoisin@uhnres.utoronto.ca&ctz=America/Toronto&gsessionid=OK

atest calendar

View and play with your data on your own computer

Download the sofware you need (see below for download and tutorial information)

Cytoscape
Enrichment Map plugin
WordCLoud plugin

View and manipulate the map using the .cys file that we give you

Put the .cys file in the directory of your choice
In Cytoscape, go to Open, File and browse the directories to locate your file and click Open.

Tips

TODO

Online tutorials

All the software used are freely available (open-source) and easy to install on your computer.

Gene-Set Enrichment Analysis (GSEA)

http://www.broadinstitute.org/gsea/index.jsp :
- Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). We use GSEA at the first analysis step. As we will perform this analysis for you, you don't need to download GSEA.

Cytoscape

http://www.cytoscape.org/:
- Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data
  Download Cytoscape 2.8.0 from http://www.cytoscape.org/download.html (need to enter, name, institution, e-mail address but no account necessary) Cytoscape tutorial: http://cytoscape.wodaklab.org/wiki/Presentations/Basic

EnrichmentMap

http://baderlab.org/EnrichmentMap
- Enrichment Map is a visualization method for gene set enrichment results which helps quickly find general functional themes in genomics data. Enrichment Map works as a plug-in for Cytoscape. To install it, download the zipped file, move it to the Cytoscape plugin directory and unzip it.

WordCloud

http://baderlab.org/WordCloud
- WordCloud is a Cytsocape plugin that generates a word tag cloud from a user-defined node selection, summarizing an attribute of choice. It notably eases the interpretation of the Enrichment Map. Download the WordCloud plugin and put the file in the Cytoscape plugin directory, unzip it and put the WordCloud.jar file in the plugin directory.

GeneMANIA

http://genemania.org
- GeneMANIA is a free public resource that offers a simple, intuitive web interface that shows the relationships between genes in a list and analyzes and extends the list to include other related genes. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function. You also can use GeneMANIA as a Cytoscape plugin. You can find the GeneMANIA tutorial at: http://genemania.org/pages/help.jsf

List of projects

This section summarizes the current projects, and the analysis status for each project is very regularly updated. You can see progress in the analysis of your project and see the different priorities assigned to each project.

date	project	lab	data received	data format OK for analysis	GSEA	First Map	Analysis report	additional analysis	status	priority
Feb 28	EZ01	Zacksenhaus	Feb 22	Feb 23	Feb 24	Feb 25	-	-	interpreting the map	1