Pathway and Network Analysis Service
Cancer Stem Cell program
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 to ensure correct input data and effective interpretation of results.
- Gene-set enrichment analysis is a useful technique to help characterize large gene lists. This technique finds functionally coherent gene-sets, such as pathways, that are statistically over-represented in a given gene list. Enrichment Map organizes gene-sets in a network. It enables the user to quickly identify the major enriched functional themes to interpret more easily the results.
- What can you expect from the service:
- We run the enrichment analysis for you and we help interpret the data.
- As we know that genomics data can overwhelming, we can accompany you at different stages:
- at the experimental design stage
- during the analysis : we offer a training session to show you how to play with your data
- after a primary analysis is done and some validations have been performed: a follow-up meeting to see if you need additional analyses or to help plan a next genomics experiment.
More Information about Pathway and Network Analysis
- 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.
- 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.
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:- If you plan a genomics experiment and you need some advice concerning the experiment design, you can book a consulting meeting.
- If you have data ready to analyze and they have been already statistically analyzed, you can book an initial 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
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! : link to calendar
Send me an e-mail at veronique.voisin@gmail.com to indicate when you want to meet and the purpose of the meeting. Im located at TMDT 8th floor on Tuesday.
- 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.
If you booked an initial meeting, please go to this link for more information: link to SOP
You must cancel a meeting 24 hours in advance. Send an e-mail at veronique.voisin@gmail.com to cancel an appointment.
Initial meeting and Data input requirement
Tutorial : How to explore an interactive Enrichment Map on your computer