liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies

Open Access

Abstract

MiRNAs are important regulators of gene expression and are frequently deregulated under pathologic conditions. They are highly stable in bodily fluids which makes them feasible candidates to become minimally invasive biomarkers. In fact, several studies already proposed circulating miRNA-based biomarkers for different types of neoplastic, cardiovascular and degenerative diseases. However, many of these studies rely on small RNA sequencing experiments that are based on different RNA extraction and processing protocols, rendering results incomparable. We generated liqDB, a database for liquid biopsy small RNA sequencing profiles that provides users with meaningful information to guide their small RNA liquid biopsy research and to overcome technical and conceptual problems. By means of a user-friendly web interface, miRNA expression profiles from 1607 manually annotated samples can be queried and explored at different levels. Result pages include downloadable expression matrices, differential expression analysis, most stably expressed miRNAs, cluster analysis and relevant visualizations by means of boxplots and heatmaps. We anticipate that liqDB will be a useful tool in liquid biopsy research as it provides a consistently annotated large compilation of experiments together with tools for reproducible analysis, comparison and hypothesis generation. ; European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [grant agreement ELBA, 765492 to M.H. and D.K.L.]; Spanish Government [AGL2017-88702-C2-2-R to M.H.]; Instituto de Salud Carlos III, FEDER funds [PIE16/00045 to J.A.M.]; Chair 'Doctors Galera-Requena in cancer stem cell research' (to J.A.M.); Ministry of Education of Spain [FPU13/05662 to R.L. and IFI16/00041 to E.A.]. Funding for open access charge: Instituto de Salud Carlos III (FEDER funds) [PIE16/00045].