HPCDb: an integrated database of pancreatic cancer

We have established a database of Human Pancreatic Cancer (HPCDb) through effectively mining, extracting, analyzing, and integrating PC-related genes, single-nucleotide polymorphisms (SNPs), and microRNAs (miRNAs), now available online at http://www.pancancer.org/ . Data were extracted from established databases, ≥5 published literature (PubMed), and microarray chips (screening of differentially expressed genes using limma package in R, |log 2 fold change (FC)| > 1). Further, protein–protein interactions (PPIs) were investigated through the Human Protein Reference Database. miRNA–target relationships were also identified using the online software TargetScan. Currently, HPCDb contains 3284 genes, 120 miRNAs, 589 SNPs, 10,139 PPIs, and 3904 miRNA–target pairs. The detailed information on PC-related genes (e.g., gene identifier (ID), symbol, synonyms, full name, chip sets, expression alteration, PubMed ID, and PPIs), miRNAs (e.g., accession number, chromosome location, related disease, PubMed ID, and miRNA–target interactions), and SNPs (e.g., SNP ID, allele, gene, PubMed ID, chromosome location, and disease) is presented through user-friendly query interfaces or convenient links to NCBI GEO, NCBI PubMed, NCBI Gene, NCBI dbSNP, and miRBase. Overall, HPCDb provides biologists with relevant information on human PC-related molecules at multiple levels, helping to generate new hypotheses or identify candidate markers.