Limiting the number of differentially expressed genes (DEGs) to 5,000 in iPathwayGuide is a deliberate statistical and practical threshold designed to ensure the integrity of your biological analysis. If thousands of genes are flagged as differentially expressed, nearly every pathway looks significant and the real signal is lost in noise. If your genes came from a differential expression analysis, upload the complete results table instead ( every measured gene with its log2 fold-change and adjusted p-value) and set your significance thresholds within iPathwayGuide. That gives the analysis the full background it needs and avoids the size limit.