To examine the functional features of NAGenes, WebGestalt [20] and Ingenuity Pathway Analysis system (IPA; https://analysis.ingenuity.com) were applied for functional enrichment analysis, including Gene Ontology (GO) term analysis and pathway analysis. WebGestalt is a web-based integrated data mining system to evaluate the significance of GO terms enrichment in the candidate genes. IPA is designed to identify global canonical pathways from a given list of genes. Basically, the genes with their symbol and/or corresponding GenBank Accession Numbers are uploaded into the IPA and compared with the genes included in each canonical pathway. All the pathways with one or more genes overlapping the candidate genes are extracted, with each of them assigned a p value to denote the probability of overlap between the pathway and the input genes via Fisher’s exact test. Then, the corresponding multiple testing correction p-value is calculated with the method of Benjamini and Hockberg, namely PBH-value [21].
