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.

Highlights

  • Tissue-specific gene expression plays a fundamental role in multi-cellular biology

  • Discovery of Tissue-Specific Genes Twelve Excel spreadsheet files were generated for the kidney, liver, lung, heart, muscle, and adipose tissue specific expression in the human and mouse, respectively

  • Three novel tissue-specific genes discovered by our method included AMDHD1 in the liver, PRUNE2 in the heart and ACVR1C in the adipose tissue

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Summary

Introduction

Tissue-specific gene expression plays a fundamental role in multi-cellular biology. About 100 to 200 signature genes are expressed in a specific tissue. A detailed understanding of the tissue-specific pattern of gene expression can help elucidate the molecular mechanisms of tissue development, gene function, and transcriptional regulation of biological processes [1]. Tissuespecific transcript analysis can indicate novel functions of known and unknown genes. The expression of tissue-specific genes can be used as an indicator for many complex diseases. Examples include the tissue-specific expression of insulin signaling-related genes in diabetes, the stroma-tumor interaction-related genes in cancer, and the tissue-specific expression of mutant IKBKAP (inhibitor of kappa light polypeptide enhancer in B cells, kinase complex-associated protein) gene in Familial Dysautonomia [2]

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