Hepamine - A Liver Disease Microarray Database, Visualization Platform and Data-Mining Resource

• Published in: Scientific reports Vol. 10; no. 1; p. 4760
• Main Authors: Itzel, Timo, Neubauer, Melanie, Ebert, Matthias, Evert, Matthias, Teufel, Andreas
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 16.03.2020; Nature Publishing Group
• Subjects: 631/114/2164; 692/4020/4021/1607; Bioinformatics; Computational Biology; Data Mining; Databases, Genetic; Datasets as Topic; DNA microarrays; Gene Expression; Gene Expression Profiling; Hepatology; Humanities and Social Sciences; Humans; Liver diseases; Liver Diseases - genetics; multidisciplinary; Oligonucleotide Array Sequence Analysis; Science; Science (multidisciplinary); Software; Translational Medical Research
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-61508-y

Numerous gene expression profiling data on liver diseases were generated and stored in public databases. Only few were used for additional analyses by the hepatology research community. This may mostly be due to limited bioinformatics knowledge of most biomedical research personnel. In order to support an easy translation of bioinformatics data into translational hepatology research, we created Hepamine, a liver disease gene expression, visualization platform and data-mining resource. Microarray data were obtained from the NCBI GEO database. Pre-analysis of expression data was performed using R statistical software and the limma microarray analysis package from the Bioconductor repository. We generated Hepamine, a web-based repository of pre-analyzed microarray data for various liver diseases. At its initial release Hepamine contains 13 gene expression datasets, 20 microarray experiments and approximately 400 000 gene expression measurements. A self-explanatory website offers open and easy access to gene expression profiles. Results are furthermore visualized in simple three-color tables indicating differential expression. All data were linked to common functional and genetic databases particularly through the DAVID bioinformatics suite. Hepamine provides comprehensive data and easy access to hepatologic gene expression data even without in depth bioinformatics or microarray profiling experience. http://www.hepamine.de.