Identification of novel tissue-specific genes by analysis of microarray databases: a human and mouse model

PLoS One. 2013 May 31;8(5):e64483. doi: 10.1371/journal.pone.0064483. Print 2013.

Abstract

Understanding the tissue-specific pattern of gene expression is critical in elucidating the molecular mechanisms of tissue development, gene function, and transcriptional regulations of biological processes. Although tissue-specific gene expression information is available in several databases, follow-up strategies to integrate and use these data are limited. The objective of the current study was to identify and evaluate novel tissue-specific genes in human and mouse tissues by performing comparative microarray database analysis and semi-quantitative PCR analysis. We developed a powerful approach to predict tissue-specific genes by analyzing existing microarray data from the NCBI's Gene Expression Omnibus (GEO) public repository. We investigated and confirmed tissue-specific gene expression in the human and mouse kidney, liver, lung, heart, muscle, and adipose tissue. Applying our novel comparative microarray approach, we confirmed 10 kidney, 11 liver, 11 lung, 11 heart, 8 muscle, and 8 adipose specific genes. The accuracy of this approach was further verified by employing semi-quantitative PCR reaction and by searching for gene function information in existing publications. Three novel tissue-specific genes were discovered by this approach including AMDHD1 (amidohydrolase domain containing 1) in the liver, PRUNE2 (prune homolog 2) in the heart, and ACVR1C (activin A receptor, type IC) in adipose tissue. We further confirmed the tissue-specific expression of these 3 novel genes by real-time PCR. Among them, ACVR1C is adipose tissue-specific and adipocyte-specific in adipose tissue, and can be used as an adipocyte developmental marker. From GEO profiles, we predicted the processes in which AMDHD1 and PRUNE2 may participate. Our approach provides a novel way to identify new sets of tissue-specific genes and to predict functions in which they may be involved.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Activin Receptors, Type I / genetics*
  • Activin Receptors, Type I / metabolism
  • Adipose Tissue / metabolism
  • Amidohydrolases / genetics*
  • Amidohydrolases / metabolism
  • Animals
  • Biomarkers / metabolism
  • Databases, Genetic
  • Gene Expression Profiling
  • Gene Expression Regulation*
  • Humans
  • Liver / metabolism
  • Mice
  • Microarray Analysis*
  • Myocardium / metabolism
  • Neoplasm Proteins / genetics*
  • Neoplasm Proteins / metabolism
  • Organ Specificity
  • Real-Time Polymerase Chain Reaction
  • Species Specificity

Substances

  • Biomarkers
  • Neoplasm Proteins
  • PRUNE2 protein, human
  • ACVR1C protein, human
  • Activin Receptors, Type I
  • Amidohydrolases

Grant support

This project was supported by Agriculture and Food Research Initiative Competitive grant number 2010-65206-20716 from the USDA National Institute of Food and Agriculture. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.