I am attempting to perform enrichment analysis of my miRNA data using the miRNet network viewer web-based application. Specifically I am attempting to obtain the KEGG pathway results of gene targets (derived from miRTarBase, TarBase, and miRecords) from my miRNA list.
I performed enrichment analysis of all genes using the empirical sampling method and querying the KEGG database. The results of the enrichment analysis provide me with the Pathway ID, Hits, pval, and FDR adj. pval. However, the pval for all 100 of the KEGG pathways is displayed as “<0.001” and the adj. pval is displayed as “0”. When the results of the enrichment analysis were downloaded, I obtained the same data categories (Pathway ID, Hits, pval, and adj. pval) and the pval and adj. pval were displayed as “0”. My first thought was to repeat the empirical sampling 5 times to improve the results, but the pval and adj. pval were still “0”. I have trouble believing these results, given that other popular programs (understanding that there are differences in methods) give me worse pval results. Could anyone advise on what I could do to improve my results? In addition, I would like to obtain more information for better visualization and interpretation of my enrichment analysis results (e.g., Gene Ratio, Bg Ratio). Is this information obtainable?
As it stands, the pval results of “0” and lack of Gene Ratio and Bg Ratio makedifficult to visualize/interpret these KEGG results using standard visualization methods such as bar charts/dotplots. I can provide any other information from my analysis that could be useful. Thank you for any input and I look forward to hearing back.