IiqDB: A small-RNAseq knowledge discovery database for liquid biopsy studies

Ernesto Aparicio-Puerta, David Jáspez, Ricardo Lebrón, Danijela Koppers-Lalic, Juan A. Marchal, Michael Hackenberg

Research output: Contribution to journalArticleAcademicpeer-review

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. LiqDB is available at http://bioinfo5.ugr.es/liqdb.
Original languageEnglish
Pages (from-to)D113-D120
JournalNucleic Acids Research
Volume47
Issue numberD1
DOIs
Publication statusPublished - 8 Jan 2019

Cite this

Aparicio-Puerta, E., Jáspez, D., Lebrón, R., Koppers-Lalic, D., Marchal, J. A., & Hackenberg, M. (2019). IiqDB: A small-RNAseq knowledge discovery database for liquid biopsy studies. Nucleic Acids Research, 47(D1), D113-D120. https://doi.org/10.1093/nar/gky981