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There are many useful visualizations, annotations, and biological interpretations that can operate on a gene list. In order for these features operate on an imported list, an annotation file must first 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^® 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.

Adding an annotation file

• Select File from the main toolbar
• Select Genomic Database under Import (Figure 1)
  
  

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The annotation file has been associated with the spreadsheet and additional tasks can now be performed on the data. 

Adding annotations

Inserting annotations from an annotation file

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In addition to SNPs, this feature can associate any data with a list of genes or genomic coordinates; the dbSNP database, any miRNA database, data from the Database of Genomic Variants (dgv), any mRNA transcriptome database, or any custom annotation source can be associated with your list. In each case, this feature will add columns to the imported gene list spreadsheet that match the genes with features from those databases.

GO Enrichment

The Gene Ontology (GO) Enrichment  p-value calculation uses either a Chi-Square or Fisher’s Exact test to compare the genes included in the significant gene list to all possible genes present in the experiment or the background genes. For a microarray experiment, background genes consists of all genes on the chip/array; for a next generation sequencing experiment, all genes in the species transcriptome are considered background genes. 

Because the calculation is essentially comparing overlapping sets of genes and does not use intensity values, GO Enrichment can be performed on an imported gene list even without any numerical values. GO Enrichment is available through the Gene Expression workflow. 

If no annotation file has been specified for the gene list, GO Enrichment will use the full species transcriptome as the background genes. While suitable for next generation sequencing experiments, for microarray experiments, only the genes on the chip/array are appropriate. Please contact our technical support department for assistance with this step if needed. 

Pathway Enrichment

Like GO Enrichment, Pathway Enrichment does not require numerical values, but instead operates on lists of genes - a list of significant genes vs. background genes. Consequently, Pathway Enrichment may be used with an imported list of genes even without any numerical values. The list of background genes is set to the species transcriptome by default, but can be set to a specific set of genes if the gene list has been associated with an annotation file.  

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