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Pathway enrichment generates a results spreadsheet, Pathway-Enrichment.txt, visible in both Partek Genomics Suite (Figure 1) and in Partek Pathway.
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Contents of the pathway enrichment spreadsheet
The spreadsheet includes 13 columns with information for each pathway represented in the source gene list.
1. Pathway Name - the name of the KEGG pathway
2. Database - the source database for the pathway annotation
3. Enrichment score - the negative natural log of the enrichment p-value derived from the contingency table (Fisher's Exact test) or the Chi-squared test
4. Enrichment p-value - the enrichment p-value derived from the contingency table (Fisher's Exact test) or the Chi-squared test
5. % genes in pathway that are present - the percentage of genes from the pathway that are present in the source gene list
6. Tissue score, 7. Replicate score, 8. Brain vs. Heart score - for each factor, interaction, and contrast in the ANVOA results spreadsheet, a separate score is calculated. This is derived form the negative log (base 10) of the average p-value for genes within the pathway for each factor. A high score indicates that the genes that fall into the pathway have a low p-value for the given factor.
9. # genes in list, in pathway - number of genes from the list in the pathway
10. # genes not in list, in pathway - number of genes from the pathway, not in the list
11. # genes in list, not in pathway - number of genes in list, not in the pathway
12. # genes, not in list, not in pathway - number of genes not in the pathway or the list that are included in KEGG database pathways for the species
13. Pathway ID - KEGG pathway ID
Tasks available in Partek Genomics Suite
In Partek Genomics Suite, we can view several new options that are available for each pathway (row) in the Pathway-Enrichment.txt spreadsheet.
- Right-click the row header of any row in the Pathway-Enrichment.txt spreadsheet (Figure 2)
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The new options include:
Export genes in pathway, which creates a child spreadsheet of Pathway-Enrichment.txt that contains all the genes from the selected pathway(s) (Figure 3). This new spreadsheet includes gene symbols and their pathway.
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