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There are many useful visualizations, annotations, and biological interpretation tools that can operate on a gene list. In order for these features work with an imported list, an annotation file must be associated with the gene list. Additionally, many operations that work with a list of significant genes (like GO- or Pathway-Enrichment) require comparison against a background of “non-significant” genes. The quickest way to accomplish both is to use the background of “all genes” for that organism provided by an annotation source like RefSeq, Ensembl, etc. in .pannot (Partek® annotationPartek annotation), .gff, .gtf, .bed, tab- or comma-delimited format. If the file is not already in a tab-separated or comma delimited format, you may import, modify, and save the file in the proper file format.
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- Select the annotation file; in this example, we select a .pannot file downloaded from Partek distributed library file repository (www.partek.com/html/libIndex.txt) – – hg19_refseq_14_01_03_v2.pannot
- Delete or rearrange the columns as necessary; we have placed the column with identifiers (should be unique ID) that correspond to our gene list first
- Select File then Save As Text File... to save the annotation file; we have named it Annotation File (Figure 2)
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This brings up the Configure Genomic Properties dialog (Figure 3).
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SubtitleText | Selecting an annotation file using the Configure Genomic Properties dialog |
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AnchorName | Configure Genomic Properties |
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- Select Browse under Annotation File
- Choose the annotation file; we have chosen Annotation File.txt
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SubtitleText | Choosing the column in the annotation file with gene symbols or microRNA names |
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AnchorName | Choose column |
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![](/download/attachments/11109540/2017-07-21%2010_30_03-Choose%20column%20containing%20gene%20symbol_microRNA%20name.png?version=1&modificationDate=1500651212075&api=v2)
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- Select the appropriate column; here the default choice of 1. Symbol is appropriate
- Select OK to return to the Configure Genomic Properties dialog
- Select the appropriate species and genome build options; we have selected Homo sapiens and hg19 (Figure 6)
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SubtitleText | The gene list is now fully configured with an annotation file and reference genome selected |
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AnchorName | Fully Configured Annotation |
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- Select OK
- Select (
) to save the spreadsheet
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SubtitleText | Adding an annotation column from the annotation file |
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AnchorName | Inserting Annotation |
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![](/download/attachments/11109540/2017-07-14%2010_42_25-Add%20Rows_Columns%20to%20Spreadsheet.png?version=1&modificationDate=1500399279229&api=v2)
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