Uncovering hidden duplicated content in public transcriptomics data

Database (Oxford). 2013 Mar 13;2013:bat010. doi: 10.1093/database/bat010. Print 2013.

Abstract

As part of the development of the database Bgee (a dataBase for Gene Expression Evolution), we annotate and analyse expression data from different types and different sources, notably Affymetrix data from GEO and ArrayExpress, and RNA-Seq data from SRA. During our quality control procedure, we have identified duplicated content in GEO and ArrayExpress, affecting ∼14% of our data: fully or partially duplicated experiments from independent data submissions, Affymetrix chips reused in several experiments, or reused within an experiment. We present here the procedure that we have established to filter such duplicates from Affymetrix data, and our procedure to identify future potential duplicates in RNA-Seq data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Genetic*
  • Gene Expression Profiling*
  • Gene Expression Regulation
  • Humans
  • Oligonucleotide Array Sequence Analysis
  • Statistics as Topic*