Another unique addition to the new version of WebGestalt includes functional categories defined by gene sets associated with diseases or drugs, inferred using our recently published software GLAD4U (11). We first downloaded the disease and drug terms from PharmGKB (23) and then used GLAD4U to derive a gene list for each term. Specifically, for a disease or drug term, GLAD4U queries the term in the MEDLINE database using the eSearch application programming interface (API) developed by the National Center for Biotechnology Information (NCBI), retrieves the corresponding publications, identifies genes associated with the publications based on the gene-to-publication link table provided by Entrez Gene, and returns genes that are significantly associated with the query term. Among all the terms downloaded from PharmGKB, GLAD4U returned at least 5 genes for 2286 disease terms and 758 drug terms. These disease or drug-associated gene sets have been added to WebGestalt. To demonstrate the usefulness of these new gene sets, we uploaded a recently published gene expression signature for colorectal cancer prognosis (24), which includes 487 genes inferred by prioritizing candidate genes identified from genomic
