Prioritizing Cancer Genes Using HodgeRank Reveals Critical Pathways in Cancer Progression

Cancer gene prioritization is critical for the development of targeted therapies. In this study, we applied the HodgeRank framework to rank cancerous genes based on their relative expression differences between normal and tumor samples, thereby enabling the systematic prioritization of genes for further analysis. Enrichment analysis and the corresponding enrichment maps revealed significant biological processes, cellular components, molecular functions, and pathways, including PI3K-Akt, MAPK, and IL-6/JAK signaling that play pivotal roles in cancer progression. These findings highlight the utility of HodgeRank in identifying biologically relevant gene rankings and critical pathways, providing a robust framework that is further supported by sensitivity analyses and cross-validation experiments.