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:
