Construction of an integrated human osteosarcoma database, HOsDb, based on literature mining, microarray analysis, and database retrieval

• Main Authors: Yifu Sun, Lishan Wang, Changkuan Li, Rui Gu, Weidong Zang, Wei Song, Peng Xia
• Format: Article
• Language: English
• Published: BMC 2020-05-01
• Series: BMC Cancer
• Subjects: Osteosarcoma; HOsDb; www.hosdatabase.com
• Online Access: http://link.springer.com/article/10.1186/s12885-020-06719-2

Abstract Background Osteosarcoma (OS) is the most frequent primary malignancy of bone with a high incidence in adolescence. This study aimed to construct a publicly available, integrated database of human OS, named HOsDb. Methods Microarray data, current databases, and a literature search of PubMed were used to extract information relevant to human OS-related genes and their transcription factors (TFs) and single nucleotide polymorphisms (SNPs), as well as methylation sites and microRNAs (miRNAs). This information was collated for constructing the HOsDb. Results In total, we identified 7191 OS tumor-related genes, 763 OS metastasis-related genes, and 1589 OS drug-related genes, corresponding to 190,362, 21,131, and 41,135 gene-TF pairs, respectively, 3,749,490, 358,361, and 767,674 gene-miRNA pairs, respectively; and 28,386, 2532, and 3943 SNPs, respectively. Additionally, 240 OS-related miRNAs, 1695 genes with copy number variations in OS, and 18 genes with methylation sites in OS were identified. These data were collated to construct the HOsDb, which is available at www.hosdatabase.com . Users can search OS-related molecules using this database. Conclusion The HOsDb provides a platform that is comprehensive, quick, and easily accessible, and it will enrich our current knowledge of OS.