The Heat Map panel shows expression values for genes that are associated with selectednodes and edges.
This allows for builds on non-Mac platforms. Added a Cancel option to the Cytoscape Download dialog, where we don't even create the Enrichment Map Viz panel if the user decides not to download. Fixed some issues in the existing code around that, so the same happens if the user cancels out or certain errors occur. You advance to the GSEA Finals with 50 of the world’s best student entrepreneurs. Win the award, become the EO GSEA Student Champion and receive.
You may select any number of nodes and/or edges in the network.Selecting an edge is equivalent to selecting the two gene set nodes that are connected to the edge.
Note
Gsea Online
“Where are my expression values?”
If there are more than 50 expression values per gene then the Compress: Data Set Median optionwill be automatically enabled. Marvel heroes download mac. Set Compress to –None– to see the original values.See below for more details.
Warning
There is a known issue on Mac where sometimes selecting a value in the Compress: combo boxhas no effect. The workaround is to click on the combo box with the mouse, hold downthe mouse button, hover the mouse pointer over the option you want, and then releasethe button.
Toolbar¶
- Expression Legend
- Click on an expression value cell in the table to show the Expression Legend. It will not be visibleuntil a value is selected.
- Shows the value range and the color gradient for the data set associated with the selectedexpression value. Note the value range may be different for different data sets.
- Genes
- All
- Shows all of the genes from all of the selected gene sets (union).
- Common
- Shows only genes that are common to all selected gene sets (intersection).
- All
- Expressions
- Values
- Shows the raw values from the expression file(s). Expression values are rounded totwo decimal places.
- Row Norm
- Row normalizes the expression values. For each value in a row of expression the meanof the row is subtracted followed by division by the row’s standard deviation.
- Log
- Takes the log of each expression value.
- Values
- Compress
- -None-
- Shows all of the expression values.
- Class: Median, Min, Max
- Only available if a class file was provided when the network was created.
- Shows a single column for each class where the value is the median, min or max of the valuesin the class.
- Data Set: Median, Min, Max
- Shows a single column for each data set where the value is the median, min or max of all thevalues.
- If the number of expressions per gene is greater than 50 then Compress: Median will beautomatically enabled.
- -None-
- Values
- When disabled only the color gradients are shown. When enabled the numeric expression values are shown.
- Expression values are rounded to two decimal places.
- Menu button
- Opens the panel options menu.
Table¶
Click on any of the column headers to sort the table by that column.
- Gene Column
- Description Column
- Sort Column
- This column is used to sort by ranks or by hierarchical clustering.
- Click the Sort button to show a menu of ranking options.
- If a data set has a rank file then the ranks will be listed in the menu.
- See Panel Menu below for details on how to load additional rank files.
- Hierarchical Clustering: Genes are clustered using a hierarchical clustering algorithm based ontheir expression values, the resulting hierarchy is then used to sort the genes.
- Expression Columns
- Shows expression values for each experiment.
- If there is more than one data set and each data set has common expression values then the valueswill only be shown once.
- If there are two or more data sets and they have different expression values then all the expressionvalues are shown.
- A colored bar that runs along the top of the expression column headers can be used to differentiatebetween the data sets. The color of the bar corresponds to the color shown next to the data setname in the main panel.
- Genes that do not have expression data are shown in gray.
- Phenotype Highlight
- The phenotypes that were entered in the Create EnrichmentMap Dialog are highlighted.
- Facetime for mac free download 2015. Leading Edge
- Genes that are part of the leading edge are highlighted in yellow.
- Available for GSEA results when a single gene set is selected.
- See below for more details.
GSEA Leading Edge¶
For every gene set that is tested for significance using GSEA there is a set of proteins in thatgene set defined as the Leading Edge. According to GSEA the leading edge is:
![Gsea Gsea](https://macmetric.com/wp-content/uploads/2019/10/mvc-free-youtube-download-for-mac.jpg)
“The subset of members that contribute most to the ES. For a positive ES, theleading edge subset is the set of members that appear in the ranked list priorto the peak score. For a negative ES, it is the set of members that appearsubsequent to the peak score.”
In essence, the leading edge is the set of genes that contribute most to the enrichment of the gene set.
For Enrichment Map, leading edge information is extracted from the GSEA enrichment resultsfiles from the column denoted as Rank at Max. Rank at max is the rank of the gene where theES score has the maximal value, i.e. the peak ES score. Everything with a better rank thanthe rank at max is part of the leading edge set.
Panel Menu¶
![Gsea Download For Mac Gsea Download For Mac](/uploads/1/2/4/3/124391145/879488995.jpg)
- Show in GeneMANIA…
- Creates a GeneMANIA network from the list of genes currently selected in the Heat Map.
- See GeneMANIA for more details.
- Show in STRING…
- Creates a STRING network from the list of genes currently selected in the Heat Map.
- See STRING for more details.
- Show in Pathway Commons…
- Opens a web browser and creates a network on the Pathway Commons painter website.
- See Pathway Commons Painter for more details.
- Add Rankings
- Opens a pop-up dialog that allows you to load an additional rank file.
- See Add Ranks Dialog below for more details.
- Export as TXT
- Export the expressions currently being viewed in the heat map table as a tab-separatedtext file. The first line of the file contains the table headers.
- If the heat map is showing the leading edge then you will be promptedto save just the genes that are part of the leading edge or all the genes.
- Export as PDF
- Export the the expressions currently being viewed in the heat map table as a PDF file.
- The visual state of the table is reflected in the PDF file. For example to show the expression valuesin the PDF file enable the show values option in the toolbar.
- Hierarchical Cluster - Distance Metric
- Allows to select the distance metric used by the hierarchical cluster algorithm.
- Auto-Focus HeatMap
- If enabled then every time a node/edge is selected the HeatMap panel will bebrought to the front.
- Disabled by default.
- Sync Data Sets with Control Panel
- If enabled then data sets that are not selected in the Control Panel will not be shown in the Heat Map.
- Enabled by default.
- Display only selected Data Sets
- If enabled then data sets that do not contain the gene sets represented by the selected nodes/edgeswill not be shown in the Heat Map.
- Enabled by default.
- Auto-sort leading edge
- If enabled then the ranking column will automatically sort the leading edge to the top.
- Enabled by default.
Add Ranks Dialog¶
Used to load additional ranks files into an existing data set.
Gsea Tutorial
GSEA (Gene Set Enrichment Analysis) is a tool for gene enrichment analysis. The GSEA algorithm assesses differences between gene sets and uses the Molecular Signatures Database (MSigDB) for annotation.
Topic
RNA-Seq; Gene expression
Details
- Operation: Gene-set enrichment analysis
- Software interface:Graphical user interface
- Language: Java
- Operating system: Microsoft Windows, Mac OS X, Linux
- License:Other Cost:Free
- Version name:- Maturity: Stable
- Credit: National Cancer Institute (NCI); Informatics Technology for Cancer Research (ITCR).
- Contact:gsea-team _at_ broadinstitute.org
- Collection: -
Publications
Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstråle M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC 'PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.' Nat Genet. 2003 Jul;34(3):267-73. https://doi.org/10.1038/ng1180
PMID: 12808457
PMID: 12808457
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP 'Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.' Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. 10.1073/pnas.0506580102. Epub 2005 Sep 30. https://doi.org/10.1073/pnas.0506580102
PMID: 16199517
PMCID: PMC1239896
PMID: 16199517
PMCID: PMC1239896
Bild A, Febbo PG 'Application of a priori established gene sets to discover biologically important differential expression in microarray data.' Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15278-9. Epub 2005 Oct 17. https://doi.org/10.1073/pnas.0507477102
PMID: 16230612
PMCID: PMC1266131
PMID: 16230612
PMCID: PMC1266131
Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov JP 'GSEA-P: a desktop application for Gene Set Enrichment Analysis.' Bioinformatics. 2007 Dec 1;23(23):3251-3. Epub 2007 Jul 20. https://doi.org/10.1093/bioinformatics/btm369
PMID: 17644558
PMID: 17644558
Download and documentation
- Source:http://software.broadinstitute.org/gsea/
downloads.jsp - Documentation:http://software.broadinstitute.org/cance
r/software/gsea/wiki/index.php/Main_Page - Home page:http://software.broadinstitute.org/gsea/
index.jsp - Data:http://software.broadinstitute.org/gsea/
msigdb/index.jsp - Links:http://www.broadinstitute.org/cancer/sof
tware/gsea/wiki/index.php/Using_RNA-
seq_Datasets_with_GSEA