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

Ernesto Aparicio-Puerta1,2,3,4, David Jáspez1,2, Ricardo Lebrón1,2

  • 1Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain.

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|October 26, 2018
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Summary

MicroRNAs (miRNAs) are key gene regulators and potential biomarkers in bodily fluids. The liqDB database standardizes small RNA sequencing data for reliable liquid biopsy research and biomarker discovery.

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Area of Science:

  • Genomics
  • Biomarker Discovery
  • Bioinformatics

Background:

  • MicroRNAs (miRNAs) regulate gene expression and are implicated in various diseases.
  • Their stability in bodily fluids makes them promising minimally invasive biomarkers.
  • Current research faces challenges due to inconsistent small RNA sequencing protocols.

Purpose of the Study:

  • To introduce liqDB, a comprehensive database for small RNA sequencing profiles from liquid biopsies.
  • To provide a standardized resource for researchers to overcome technical and conceptual hurdles in miRNA biomarker studies.
  • To facilitate exploration and analysis of miRNA expression data from diverse clinical samples.

Main Methods:

  • Generation of a manually annotated database (liqDB) comprising 1607 liquid biopsy small RNA sequencing profiles.
  • Development of a user-friendly web interface for querying and exploring miRNA expression data.
  • Implementation of tools for differential expression analysis, stability assessment, clustering, and visualization (boxplots, heatmaps).

Main Results:

  • A large, consistently annotated compilation of liquid biopsy small RNA sequencing experiments is now available.
  • The database allows users to access downloadable expression matrices and perform various analyses.
  • Standardized data facilitates comparison across studies and aids in hypothesis generation.

Conclusions:

  • liqDB serves as a valuable resource for advancing liquid biopsy research.
  • It promotes reproducible analysis and comparison of miRNA expression profiles.
  • The database supports the identification and validation of circulating miRNA biomarkers.