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.

How to use the service

Who can use the service

• You can use the service if you are a member of Cancer Stem Cell program, if you are planning to generate omics data, or if you already have large gene lists coming from large-scale 'omics' (e.g. genomics) projects that are ready to be analyzed. Please, book an appointment with us for an initial meeting, a consulting meeting or a training session (see description below).
• If you have data ready to analyze and they have been already statistically analyzed, you can book an initial meeting.
• If you plan a genomics experiment and you need some advice concerning the experiment design, you can book a consulting meeting.
• If you want to do your enrichment analyses on your own, you can book a training session and we can explain you how to use Enrichment Map, Word Cloud and GeneMANIA.

How to book an appointment

1. Look at the calendar below to see my available times the day you want to meet (30 min to 1 h meeting). Be aware of that I'm available for meetings only on Tuesdays!

2. Send me an e-mail at veronique.voisin@gmail.com to indicate when you want to meet and the purpose of the meeting.

3. I will send you an e-mail back to confirm the appointment.
4. If we meet for the first time, I encourage you to send me a paper that best describe your work prior to our meeting.

5. 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: please have these data and information ready

link to SOP

Calendar

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

How to explore an interactive Enrichment Map on your computer

link to tutorial page

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.

? Link to results and reports ?