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Enrichment analysis is a technique commonly used to add biological context to a list of genes, such as list of significant genes filtered from differential analysis report. The procedure is based on assigning genes to groups and then finding overrepresented groups in filtered gene lists using a Fisher's exact test.
Running Gene set
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Enrichment
Gene set enrichment task can be invoked on a differential analysis output (or filtered differential analysis output) data node or filtered count matrix data node. Since the data node including all the features will server as serve as background, to get a meaningful result, always use a data node containing subset of features to invoke this task. Only gene names will be used in the computation.
- Click a Feature list data node
- Click the Biological interpretation section of the toolbox
- Click Gene set enrichment
- There are two options for Database. KEGG database requires a special license (Figure 1).
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SubtitleText | Selecting KEGG database |
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AnchorName | Gene set selection |
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- When chooseGene set database, it database is user defined database, see the more details in the Adding a Gene Set chapter. The gene sets available for the current Assembly are listed under the Gene set database drop-down list (Figure 2). The assembly is automatically selected, if possible. If the assembly cannot be detected, you can specify it using a the drop-down menu.
Partek distribute distributes Gene Ontology (GO) for human and mouse genomes, a bioinformatics initiative to unify the representation of gene and gene product attributes across various species [1, 2].
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SubtitleText | Selecting user defined gene set database |
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AnchorName | Create gene list dialog |
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- Select feature identifier (optional) can be used to specify the feature format (e.g. Gene name, Gene ID, Feature ID).
- Specify the background gene list (optional) can be used for a feature list. Select the list using the drop-down. Click here for more information on List management.
The background gene list is used as the list of possible genes. By default, this is the genes included in the selected gene set database. If your assay limits the genes that could be detected, you may want to specify a background list.
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SubtitleText | Go enrichment report (truncated). Gene set column contains Gene Ontology identifiers (hyperlinks). Category labels are in the Description column. Enrichment score: negative natural logarithm of the enrichment P-value derived from the Fisher's exact test. Genes in list: number of genes that are present both in the list of significant genes and the gene set (GO category). Genes not in list: number of genes that are present in the gene set, but are not present in the list of significant genes. The column on the right contains links to gene breakdown chart and extra details |
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AnchorName | Go enrichment report |
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The contingency table (Figure 4) can be displayed by selecting the View gene breakdown chart icon on the right (
). The term "list" refers to the list of significant genes, while the term "set" refers to the respective GO category. The first row of the contingency table is also seen in the report, namely the Genes in list and Genes not in list columns.
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SubtitleText | Contingency table used to calculate the enrichment p-value. List refers to the list of significant genes, set refers to the gene ontology category |
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AnchorName | Contingency table |
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The View extra details (
) button provides additional information on the GO category (Figure 5). In addition to the details already given in the report, a full list of Genes in list and Genes not in list can be inspected and downloaded (Download data) to the local computer as a text file. Use the arrow to expand these sections.
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SubtitleText | Gene ontology enrichment extra details |
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AnchorName | Extra enrichment details |
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As previously mentioned, if you are using the GO gene sets distributed by Partek, the GO identifiers in the first column are hyperlinks to the Gene Ontology web-site entries (an example shown in Figure 6).
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SubtitleText | Selecting a GO category in the table report opens up a browser and displays additional information on that category via GO web-page |
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AnchorName | GO category selection |
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![](/download/attachments/2261149/amigo_webpage.png?version=1&modificationDate=1467420428618&api=v2)
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When KEGG database is used, on the enrichment task report, when click on a pathway ID in the Gene set column, a KEGG pathway gene network picture is displayed (Figure 7).
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SubtitleText | KEGG pathway map |
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AnchorName | KEGG pathway map |
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![](/download/attachments/2261149/1.png?version=1&modificationDate=1661204178205&api=v2)
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- Fixed color: all genes are colored black.
- Genes in list: all genes in the list are colored, default color is yellow, but this can be configured. Genes not in the list are black.
- Statistics in the gene list: .e.g FDR, p-value, Fold change etc. Colors can be customized by clicking on the color square to change.
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Feature details
Mousing over a rectangle shows the genes indicated by the rectangle in the tooltip (Figure 8). Genes are listed on rows with all aliases in the KEGG database included on the row. Genes that are in the list are shown in bold. The gene being used to color the rectangle is shown in red.
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SubtitleText | Checking genes represented by a rectangle |
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AnchorName | checking genes |
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![](/download/attachments/2261149/2.png?version=1&modificationDate=1661204201560&api=v2)
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On KEGG pathway maps that include chemical compounds, the chemical structure is shown in the tooltip on mouse-over (Figure 109).
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SubtitleText | Viewing chemical compound |
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AnchorName | compound |
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![](/download/attachments/2261149/3.png?version=1&modificationDate=1661204215281&api=v2)
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If the gene set enrichment table has fewer than 100 results (rows), the GO categories can be visualized in the Data Viewer. Otherwise, a notification is displayed in the top left corner (Figure 1110).
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SubtitleText | If the gene ontology table has more than 100 rows, visualization of results is not possible |
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AnchorName | go_warning |
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If needed, filter down the number results, for instance by using a cut-off based on the enrichment score. Type in the cut-off value in the text box beneath the Enrichment score and hit enter (an example is shown in Figure 1211). Once the number or results falls below 100, a link to the Data Viewer will be displayed (Figure 8). Click on the View plots in Data Viewer link to open a new Data Viewer session.
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SubtitleText | Use the View plots in Data Viewer link to visualize the gene ontology enrichment results. The link is not visible if the table contains more than 100 rows |
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AnchorName | view_plots_data_viewer_link |
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Two plots are loaded into Data Viewer (Figure 1312). Both plots show enrichment score on the horizontal axis and gene ontology categories (i.e. the ones present in the gene enrichment table) on the vertical axis. The plots show enrichments scores (Enrichment score column of the gene ontology table) and - in addition - the plot on the left uses color range to depict enrichment P-value (green = low, red = high P-value).
The same functionality is available for pathway enrichment results.
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SubtitleText | Visualizing gene ontology results. Vertical axis shows the gene ontology categories present in the underlying gene ontology table |
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AnchorName | enrichment_plot |
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References
- Ashburner M, Ball CA, Blake JA et al. Gene Ontology: tool for the unification of biology. Nat Genetics. 2000; 25:25-29.
- The Gene Ontology Consortium. Gene Ontology Consortium: going forward. Nucleic Acids Res. 2015; 43:D1049-1056.Recommended citations from the Geneontology.org website
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