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| = Pathway and Network Analysis Service = {{attachment:Software/EnrichmentMap/UserManual/enrichmentmap_logo3.png|Enrichment Map Logo|align="right"}}<<BR>> == Cancer Stem Cell program == |
= OICR Cancer Stem Cell program - Pathway and Network Analysis Service = |
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* '''The Pathway and Network Analysis Service''' is freely available to all Cancer Stem Cell program members. <<BR>> * '''High-throughput genomic experiments''' (e.g. gene expression, large-scale genetic screens) often lead to the identification of large gene lists. The interpretation of results and the formulation of consistent biological hypotheses from these gene lists can be challenging. Computational 'pathway and network analysis' approaches can aid interpretation by relating the gene list to knowledge about the biological system, such as pathways. |
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| == Introduction about the service: == | * '''Our goal''' is to help researchers interpret results of genomics experiments. Analysis is conducted in close collaboration with researchers on each project to ensure correct input data and effective interpretation of results. Ideally researchers do as much of the analysis and interpretation as they can. |
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| * The Pathway and Network Analysis Service is freely available to all Cancer Stem Cell program members. <<BR>> * 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. <<BR>> The interpretation of results and the formulation of consistent biological hypotheses from these gene lists are challenging.<<BR>> Computational approaches can aid interpretation by relating the gene lists to knowledge about the biological system. |
* '''Standard types of pathway analysis offered''' * '''Find pathways enriched in a list of genes (e.g. differentially expressed genes)''' Gene-set enrichment analysis helps characterize large gene lists by finding functionally coherent gene-sets, such as pathways, that are statistically over-represented in a given gene list. We have also developed a method to visualize the results of this analysis, called Enrichment Map. '''Input''': gene list from genomics experiment (statistically analyzed). '''Output''': enriched pathways visually displayed. * Related publications: [[http://www.ncbi.nlm.nih.gov/pubmed/16199517|Gene-set enrichment analysis (GSEA)]] [[http://www.ncbi.nlm.nih.gov/pubmed/21085593|Enrichment Map]] * '''Predict the function of an unknown gene''' GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. '''Input''': a gene or set of genes. '''Output''': connections between input genes and suggestions for additional related genes. * Related publications: [[http://www.ncbi.nlm.nih.gov/pubmed/20576703|GeneMANIA]] * '''We can discuss custom analysis''' |
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| * 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 be overwhelming, we can accompany you at different stages: |
* '''What can you expect from the service:''' * We run the analysis for you and help interpret the data. * We can help you at different stages: |
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| * 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 can be booked to see if you need additional analyses or to help plan a next genomics experiment. |
* during the analysis: we offer training in data analysis and exploration * after an initial analysis is complete and any validation experiments have been performed, we can book a follow-up meeting to see if you need additional analyses or to help plan subsequent genomics experiments. |
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== 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. http://www.ncbi.nlm.nih.gov/pubmed/21085593 * 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 * [[CancerStemCellProject/VeroniqueVoisin/PathwayAnalysisService/Information | Link to more information ]] ---- ----- {{attachment:flowchart.png|flowchart|align="right"}} |
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| * '''Members of the OICR Cancer Stem Cell program''' may use the service if * You are planning to generate 'omics' (e.g. gene expression) data * You have a large gene list derived from a large-scale omics project that is ready to be analyzed * You require training in pathway and network analysis |
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| <<BR>> '''Please schedule an appointment with us:''' * '''Consulting meeting''' If you are planning a genomics experiment and you need some advice concerning the experiment design. Typical time: 30-60 minutes |
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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. <<BR>> 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. |
* '''Analysis planning meeting''' If you have data ready to analyze and they have been already statistically analyzed. Typical time: 60 minutes |
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| * 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. | * '''Training session''' If you want to do your own pathway and network analyses, we can explain how various state of the are software tools and methods work, such as GSEA, Enrichment Map and GeneMANIA. Typical time: Regular training schedule is currently being planned. Individual or group sessions can be arranged. |
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| 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! : [[CancerStemCellProject/VeroniqueVoisin/PathwayAnalysisService/Calendar | 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. I'm 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: [[CancerStemCellProject/VeroniqueVoisin/PathwayAnalysisService/SOP | 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. |
1. Normal in person meetings are on Tuesdays at TMDT 8th floor. Let us know if this doesn't work for you. [[CancerStemCellProject/VeroniqueVoisin/PathwayAnalysisService/Calendar |Check our meeting calendar to see available times]] (30 min to 1 h meeting) *Send an e-mail to veronique.voisin@gmail.com with your preferred meeting time and the purpose of the meeting and wait for e-mail confirmation. *For first-time meetings, please send a paper that best describes your work prior to the meeting. *If you booked an initial meeting, please [[CancerStemCellProject/VeroniqueVoisin/PathwayAnalysisService/SOP| read our standard operating procedure to know what to expect]] *If you must cancel a meeting, please give 24 hours notice to veronique.voisin@gmail.com. |
OICR Cancer Stem Cell program - Pathway and Network Analysis 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, large-scale genetic screens) often lead to the identification of large gene lists. The interpretation of results and the formulation of consistent biological hypotheses from these gene lists can be challenging. Computational 'pathway and network analysis' approaches can aid interpretation by relating the gene list to knowledge about the biological system, such as pathways.
Our goal is to help researchers interpret results of genomics experiments. Analysis is conducted in close collaboration with researchers on each project to ensure correct input data and effective interpretation of results. Ideally researchers do as much of the analysis and interpretation as they can.
Standard types of pathway analysis offered
Find pathways enriched in a list of genes (e.g. differentially expressed genes) Gene-set enrichment analysis helps characterize large gene lists by finding functionally coherent gene-sets, such as pathways, that are statistically over-represented in a given gene list. We have also developed a method to visualize the results of this analysis, called Enrichment Map. Input: gene list from genomics experiment (statistically analyzed). Output: enriched pathways visually displayed.
Related publications: Gene-set enrichment analysis (GSEA) Enrichment Map
Predict the function of an unknown gene GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Input: a gene or set of genes. Output: connections between input genes and suggestions for additional related genes.
Related publications: GeneMANIA
We can discuss custom analysis
What can you expect from the service:
- We run the analysis for you and help interpret the data.
- We can help you at different stages:
- at the experimental design stage
- during the analysis: we offer training in data analysis and exploration
- after an initial analysis is complete and any validation experiments have been performed, we can book a follow-up meeting to see if you need additional analyses or to help plan subsequent genomics experiments.
How to use the service
Who can use the service
Members of the OICR Cancer Stem Cell program may use the service if
- You are planning to generate 'omics' (e.g. gene expression) data
- You have a large gene list derived from a large-scale omics project that is ready to be analyzed
- You require training in pathway and network analysis
Please schedule an appointment with us:Consulting meeting If you are planning a genomics experiment and you need some advice concerning the experiment design. Typical time: 30-60 minutes
Analysis planning meeting If you have data ready to analyze and they have been already statistically analyzed. Typical time: 60 minutes
Training session If you want to do your own pathway and network analyses, we can explain how various state of the are software tools and methods work, such as GSEA, Enrichment Map and GeneMANIA. Typical time: Regular training schedule is currently being planned. Individual or group sessions can be arranged.
How to book an appointment
Normal in person meetings are on Tuesdays at TMDT 8th floor. Let us know if this doesn't work for you. Check our meeting calendar to see available times (30 min to 1 h meeting)
Send an e-mail to veronique.voisin@gmail.com with your preferred meeting time and the purpose of the meeting and wait for e-mail confirmation.
- For first-time meetings, please send a paper that best describes your work prior to the meeting.
If you booked an initial meeting, please read our standard operating procedure to know what to expect
If you must cancel a meeting, please give 24 hours notice to veronique.voisin@gmail.com.
Initial meeting and Data input requirement
Tutorial : How to explore an interactive Enrichment Map on your computer