DAG expression: high-throughput gene expression analysis of real-time PCR data using standard curves for relative quantification

PLoS One. 2013 Nov 18;8(11):e80385. doi: 10.1371/journal.pone.0080385. eCollection 2013.

Abstract

Background: Real-time quantitative PCR (qPCR) is still the gold-standard technique for gene-expression quantification. Recent technological advances of this method allow for the high-throughput gene-expression analysis, without the limitations of sample space and reagent used. However, non-commercial and user-friendly software for the management and analysis of these data is not available.

Results: The recently developed commercial microarrays allow for the drawing of standard curves of multiple assays using the same n-fold diluted samples. Data Analysis Gene (DAG) Expression software has been developed to perform high-throughput gene-expression data analysis using standard curves for relative quantification and one or multiple reference genes for sample normalization. We discuss the application of DAG Expression in the analysis of data from an experiment performed with Fluidigm technology, in which 48 genes and 115 samples were measured. Furthermore, the quality of our analysis was tested and compared with other available methods.

Conclusions: DAG Expression is a freely available software that permits the automated analysis and visualization of high-throughput qPCR. A detailed manual and a demo-experiment are provided within the DAG Expression software at http://www.dagexpression.com/dage.zip.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Genetic
  • Gene Expression / genetics
  • Gene Expression Profiling / methods*
  • High-Throughput Screening Assays / methods*
  • Real-Time Polymerase Chain Reaction / methods*
  • Software
  • Statistics as Topic / methods*

Grant support

This work was supported by the Innovation Consolider-Ingenio 2010 Program (CSD2007-00036, Centre for Research in Agricultural Genomics), and by MICINN project AGL2011-29821-C02 (Ministerio de Economía y Competitividad). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.