Computational protocol: Integrated miRNA-mRNA spatial signature for oral squamous cell carcinoma: a prospective profiling study of Narrow Band Imaging guided resection

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[…] Gene set enrichment analysis of biological pathways associated with differentially expressed miRNAs was performed using the miEAA tool (https://ccb-compute2.cs.uni-saarland.de/mieaa_tool/). For pathway analysis of the differentially expressed mRNA genesets we used GSEA hosted at the Broad Institute (https://genepattern.broadinstitute.org/gp/). The KEGG (Kyoto Encyclopedia of Genes and Genomes pathway) and Reactome curated pathway genesets from Molecular Signature Database (MsigDB, http://www.broadinstitute.org/gsea/msigdb/) were used. For GSEA gene differentially expressed gene lists were pre-ranked by logarithm transformation of p-value (base 10) and application of the sign of the fold-change (i.e. upregulated genes given positive values). Overrepresentation analysis (ORA) of differentially expressed genes derived from the integrated miRNA-mRNA data for pathways and gene ontology terms was performed using the web based platform EnrichR (http://amp.pharm.mssm.edu/Enrichr) which permits interrogation of multiple databases. Up and down regulated gene lists were evaluated for significant enrichment against the following gene set libraries: GO Biological Process, GO Cellular Component, GO Molecular Function (all from http://www.geneontology.org), the Wikipathways database (http://www.wikipathways.org/) and KEGG (http://www.kegg.jp/kegg) (all current as of May 2017). Enriched annotations/pathways were selected/ranked based upon combined score which was calculated by the EnrichR platform following Z-score permutation background correction on the Fischer Exact Test p-value. In order to facilitate the interpretation of GO analysis the selected output annotation lists were further consolidated and summarised using REVIGO, a tool that removes redundant terms based upon similarity. Network analysis was performed using Cytoscape 3.5.1 and the Wikipathways plugin. […]

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