|
Size: 4608
Comment:
|
← Revision 31 as of 2015-03-19 13:59:23 ⇥
Size: 7596
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| #acl CscGroup:read,write,revert | ## page was renamed from CancerStemCellProject/VeroniqueVoisin/PathwayAnalysisService/Tutorials #acl All:read |
| Line 3: | Line 4: |
| == How to explore an interactive Enrichment Map on your computer == | = RESOURCES = |
| Line 5: | Line 6: |
| == Examples of pathway maps included as figures in published papers == * 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]] * [[ Software/EnrichmentMap/Description | EnrichmentMap Description ]] *Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acutemyeloid leukemia cells. Jhas B, Sriskanthadevan S, Skrtic M, Sukhai MA, Voisin V, Jitkova Y, Gronda M, Hurren R, Laister RC, Bader GD, Minden MD, Schimmer AD.PLoS One. 2013;8(3):e58367. Epub 2013 Mar 8. *Attenuation of miR-126 activity expands HSC in vivo without exhaustion. Lechman ER, Gentner B, van Galen P, Giustacchini A, Saini M, Boccalatte FE, Hiramatsu H, Restuccia U, Bachi A, Voisin V, Bader GD, Dick JE, Naldini L.Cell Stem Cell. 2012 Dec 7;11(6):799-811. *A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals.Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, Voisin V, Bader GD, Blencowe BJ, Pearson BJ. Stem Cells. 2012 Aug;30(8):1734-45. *Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ERα- breast cancer. Liu JC, Voisin V, Bader GD, Deng T, Pusztai L, Symmans WF, Esteva FJ, Egan SE, Zacksenhaus E. Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5832-7. Epub 2012 Mar 28. *[[CSCPathwayAnalysisService/Publication | LINK TO EXAMPLES ]] *[[attachment:mapexamples.pdf | MORE ENRICHMENT MAPS FROM PUBLISHED PAPERS]] = Online tutorials = All the software used are freely available (open-source) and easy to install on your computer. === R === * install R (http://www.r-project.org/) * install RStudio (http://www.rstudio.com/) * on line tutorial :http://www.cyclismo.org/tutorial/R/ === 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, such as those in a pathway, shows statistically significant, concordant differences between two biological states (e.g. phenotypes). === Cytoscape === * http://www.cytoscape.org/: Cytoscape is a 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 the latest version of Cytoscape from http://www.cytoscape.org/download.html (you need to enter, name, institution, e-mail address but no account is necessary) Cytoscape tutorial: http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape === EnrichmentMap === * http://baderlab.org/Software/EnrichmentMap Enrichment Map is a visualization method for gene set enrichment results which helps quickly find functional themes in genomics data. Enrichment Map works as a plug-in for Cytoscape. Enrichment map can be installed from the Cytoscape plugin manager, or from the Enrichment Map download site listed above. === WordCloud === * http://baderlab.org/Software/WordCloudPlugin !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. !WordCloud can be installed from the Cytoscape plugin manager, or from the !WordCloud download site listed above. === GeneMANIA === *http://genemania.org GeneMANIA provides 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 = How to explore an interactive Enrichment Map on your computer = |
|
| Line 10: | Line 59: |
| * WordCLoud plugin | * !WordCloud plugin |
| Line 12: | Line 61: |
=== Explore the Enrichment map using the .cys file that we give you === |
=== Explore the Enrichment map using the Cytoscape session (.cys) file that we give you === |
| Line 15: | Line 63: |
| * 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. |
* Save the .cys file in the directory of your choice * In Cytoscape, go to File->Open and browse to locate your .cys file and click Open. |
| Line 26: | Line 74: |
| === Tips === * Click on “View -> Show Graphics Details” in Cytoscape to see the map details even on low zoom-levels * Please follow [[CSCPathwayAnalysisService/Tutorials/Tips | THIS LINK ]] to get tips on how to use EnrichmentMap and Cytoscape based on frequently asked questions and known issues. |
|
| Line 27: | Line 78: |
| = Additional Resources = * Please follow [[CancerStemCellProject/VeroniqueVoisin/AdditionalResources | THIS LINK ]] to find additional bioinformatics and biostatistics resources based on frequently asked questions |
|
| Line 28: | Line 81: |
| === Tips === * Click on “View / Show Graphics Details” to see the map details even on low zoom-levels |
= Training Courses = *'''SLIDES''': * Biostatistics and Bioinformatics workshop December 2011 (lecture material and hands-on session) *[[attachment:training_fall2011_dec16.pdf]] *[[attachment:hands-on_training.zip]] * CBW workshop May 2013 *[[attachment:CBW_BICG_May_2013.pdf]] * Baderlab workflow June 2013: *[[attachment:baderlab_workflow_2013.pdf]] * The Pathway and Network Analysis service recommends the [[http://bioinformatics.ca/workshops|Pathway and Network Analysis of -omics Data course]] offered annually by the Canadian Bioinformatics Workshop series: [[http://bioinformatics.ca/workshops|{{attachment:cbw-horizontal.jpg}}]] |
| Line 33: | Line 97: |
== Online tutorials == |
[[CSCPathwayAnalysisService/SOP | BACK TO STANDARD OPERATING PROCEDURE (SOP) ]] |
| Line 37: | Line 100: |
| 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 ---- ----- |
[[CSCPathwayAnalysisService | BACK TO HOME PAGE ]] |
RESOURCES
Examples of pathway maps included as figures in published papers
Related publications: Gene-set enrichment analysis (GSEA) Enrichment Map
- Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acutemyeloid leukemia cells. Jhas B, Sriskanthadevan S, Skrtic M, Sukhai MA, Voisin V, Jitkova Y, Gronda M, Hurren R, Laister RC, Bader GD, Minden MD, Schimmer AD.PLoS One. 2013;8(3):e58367. Epub 2013 Mar 8.
- Attenuation of miR-126 activity expands HSC in vivo without exhaustion. Lechman ER, Gentner B, van Galen P, Giustacchini A, Saini M, Boccalatte FE, Hiramatsu H, Restuccia U, Bachi A, Voisin V, Bader GD, Dick JE, Naldini L.Cell Stem Cell. 2012 Dec 7;11(6):799-811.
- A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals.Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, Voisin V, Bader GD, Blencowe BJ, Pearson BJ. Stem Cells. 2012 Aug;30(8):1734-45.
- Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ERα- breast cancer. Liu JC, Voisin V, Bader GD, Deng T, Pusztai L, Symmans WF, Esteva FJ, Egan SE, Zacksenhaus E. Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5832-7. Epub 2012 Mar 28.
Online tutorials
All the software used are freely available (open-source) and easy to install on your computer.
R
install R (http://www.r-project.org/)
install RStudio (http://www.rstudio.com/)
on line tutorial :http://www.cyclismo.org/tutorial/R/
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, such as those in a pathway, shows statistically significant, concordant differences between two biological states (e.g. phenotypes).
Cytoscape
- Cytoscape is a 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 the latest version of Cytoscape from http://www.cytoscape.org/download.html (you need to enter, name, institution, e-mail address but no account is necessary) Cytoscape tutorial: http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape
- Cytoscape is a 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/Software/EnrichmentMap
- Enrichment Map is a visualization method for gene set enrichment results which helps quickly find functional themes in genomics data. Enrichment Map works as a plug-in for Cytoscape. Enrichment map can be installed from the Cytoscape plugin manager, or from the Enrichment Map download site listed above.
WordCloud
http://baderlab.org/Software/WordCloudPlugin
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. WordCloud can be installed from the Cytoscape plugin manager, or from the WordCloud download site listed above.
GeneMANIA
GeneMANIA provides 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
How to explore an interactive Enrichment Map on your computer
Download the sofware you need (see below for download and tutorial information)
- Cytoscape
- Enrichment Map plugin
WordCloud plugin
Explore the Enrichment map using the Cytoscape session (.cys) file that we give you
- Download the .cys file
- Save the .cys file in the directory of your choice
In Cytoscape, go to File->Open and browse to locate your .cys file and click Open.
- Explore the map
- The “Parameters” tab in the “Results Panel” on the right side of the window contains a legend mapping the colours to the phenotypes and displaying the parameters used to create the map (cut-off values and data files).
- The “Network” tab in the “Control Panel” on the left lists all available networks in the current session and at the bottom has a overview of the current network which allows to easily navigate in a network even at higher zoom levels by dragging the blue rectangle (the current view) over the network.
- Clicking on a node (the circle that represents a gene set) will open the “EM Geneset Expression Viewer” tab in the “Data Panel” showing a heatmap of the expression values of all genes in the selected gene set.
- Clicking on an edge (the line between two nodes) will open the “EM Overlap Expression Viewer” tab in the “Data Panel” showing a heatmap of the expression values of all genes both gene sets that are connected by this edge have in common.
- If several nodes and edges are selected (e.g. by dragging a selection box around the desired gene sets) the “EM Geneset Expression Viewer” will show the union of all genes in the selected gene sets and the “EM Overlap Expression Viewer” will show only those genes that all selected gene sets have in common.
- The “Geneset Summary” tab in the “Results Panel” on the right contains information about which nodes and edges are selected.
Tips
Click on “View -> Show Graphics Details” in Cytoscape to see the map details even on low zoom-levels
Please follow THIS LINK to get tips on how to use EnrichmentMap and Cytoscape based on frequently asked questions and known issues.
Additional Resources
Please follow THIS LINK to find additional bioinformatics and biostatistics resources based on frequently asked questions
Training Courses
SLIDES:
- Biostatistics and Bioinformatics workshop December 2011 (lecture material and hands-on session)
- CBW workshop May 2013
- Baderlab workflow June 2013:
The Pathway and Network Analysis service recommends the Pathway and Network Analysis of -omics Data course offered annually by the Canadian Bioinformatics Workshop series:
