CSCPathwayAnalysisService - Bader Lab @ The University of Toronto

What you can expect

TODO

How to use the service

Who can use the service

You can use the service if you a member of Cancer Stem Cell program (http://www.cancerstemcells.ca). (Note:ask Melissa if I can use this URL). If you have large gene lists coming from large-scale 'omics' (e.g. genomics) projects that are ready to be analyzed (see section Data input requirement below), you can book an appointment with us for an initial meeting.

How to book an appointment

Look at the calendar below to see my available times the day you want to meet (30 min to 1 h meeting). Be aware that I'm available for meetings only on Tuesdays!
Send me an e-mail at veronique.voisin@gmail.com to indicate when you want to meet and the purpose of the meeting.
I will send you an e-mail back to confirm the appointment.
If we meet for the first time, I encourage you to send me a paper that best describe your work prior to our meeting.
You must cancel a meeting 24 hours in advance. send an e-mail at veronique.voisin@gmail.com to cancel an appointment.

Data input requirement

Your data should have been statistically analyzed.
Information I need to know
Files you need to give
- a ranked file (.RNK)
- an expression matrix file (.txt)

Service SOP

Standard input requirements

Calendar

private and public available https://www.google.com/calendar/embed?src=i6u58gktnv6b3ulah4kmte0me0@group.calendar.google.com&ctz=America/Toronto&gsessionid=sNRY31YmOPjvR9zF6N9llA

only public events available

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

Suggested readings