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| located at TMDT 8th floor each Tuesday | located at TMDT 8th floor on Tuesday |
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| We are developing a new pathway and network bioinformatics analysis service to help CSC program researchers. High-throughput genomic experiments (e.g. gene expression, protein expression, molecular interactions, large-scale genetic screens and other omics data) often 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. Pathway and network analysis can ease the interpretation of this data and formulation of consistent biological hypotheses. |
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. |
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All the software used are freely available (open-source). |
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| == Information about the software we use (software and tutorials) == === GSEA === |
== Online tutorials == === 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. |
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| * 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 |
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| * 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. |
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| * 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. |
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Pathway and Network Analysis Service
Cancer Stem Cell program
Veronique Voisin
- 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
- All the software used are freely available (open-source).
Online tutorials
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
- 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
- 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
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
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
Service SOP
Standard input requirements
How to use the service
- how to book an appointment
- calendar
List of projects
? Link to results and reports ?