MetaOmixTools: a user-friendly web suite for meta-analysis of ranked features and functional enrichment

ABSTRACT The growing number of omics datasets in public repositories provides an opportunity to enhance data reusability through data integration; however, complex statistical barriers often hinder the effective combination of independent studies. To address this problem, we present MetaOmixTools, an interactive web-based suite that streamlines the meta-analysis of ranked feature lists and functional enrichment profiles. The platform integrates two primary modules - MetaRank and MetaEnrich within a code-free environment. MetaRank generates robust consensus rankings from multiple lists by implementing weighted (e.g., Rank Product) and unweighted (e.g., Robust Rank Aggregation) strategies, while MetaEnrich performs functional meta-analyses by combining probability values from individual over-representation analyses using established statistical techniques. Using case studies, we established consensus rankings for acute spinal cord injury across heterogeneous platforms, identifying conserved inflammatory marker genes in the upregulated gene list (e.g., Slpi, Ccl2, Msr1) and synaptic loss genes in the downregulated gene list (e.g., Kcna2, Dao, Ppp1r1b), and also characterized inverse functional intersections between melanoma brain metastasis and neurodegenerative diseases. By providing intuitive, real-time visualization and reproducible workflows, MetaOmixTools empowers the research community to extract consistent biological insights from multi-study data. We have made MetaOmixTools freely available at https://bioinfo.cipf.es/metaomixtools/. Competing Interest Statement The authors have declared no competing interest. Footnotes Updated all versions in the manuscript + adding new authors