Comparison of gene expression profiles among papilla, medulla and cortex in rat kidney

Kotaro Tamura, Atsushi Ono, Toshikazu Miyagishima, Taku Nagao, Tetsuro Urushidani

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

The aim of this study was to compare gene expression profiles in the different kidney regions as the basis for toxicogenomics. Rat kidney was separated into papilla, medulla and cortex, and total RNA was isolated from these and from the whole slice. Gene expression profiling was performed using Affymetrix Rat Genome 230 2.0 Array. When global normalization was applied, the expression of β-actin or GAPDH varied among the regions. It was considered that such a comparison could not be made, especially between papilla and other portions, since the production of total mRNA in the former was relatively low. In fact, ANOVA was performed on the gene expression values with global normalization in papilla, medulla, cortex, and whole slice, and the numbers of genes appeared to be the highest in papilla. It was also observed that many genes showed their maximum or minimum in the whole slice, which was theoretically impossible. To overcome the problems associated with global normalization, the "percelome" normalization (a way to obtain the values directly related to the copies of mRNA per cell) was employed to compare the regions. In applying this procedure, probe sets with regional difference in expression were efficiently extracted by ANOVA. When they were sorted by the fold difference to other regions, the higher rank was occupied by genes characteristic of the functions of kidney, i.e., channels, transporters and metabolic enzymes. Some of them were consistent with the literature and were related to pathophysiological phenomena. Comprehensive comparison of data of gene expression in the renal anatomical area will greatly enhance studies of the physiological function and mechanism of toxicity in kidney.

Original languageEnglish
Pages (from-to)449-469
Number of pages21
JournalJournal of Toxicological Sciences
Volume31
Issue number5
DOIs
Publication statusPublished - Dec 2006
Externally publishedYes

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Transcriptome
Gene expression
Rats
Genes
Kidney
Analysis of variance (ANOVA)
Analysis of Variance
Messenger RNA
Toxicogenetics
Gene Expression
Toxicity
Actins
Gene Expression Profiling
RNA
Genome
Enzymes

Keywords

  • Gene expression
  • Kidney
  • Rat
  • Regional difference
  • Toxicogenomics

ASJC Scopus subject areas

  • Toxicology

Cite this

Comparison of gene expression profiles among papilla, medulla and cortex in rat kidney. / Tamura, Kotaro; Ono, Atsushi; Miyagishima, Toshikazu; Nagao, Taku; Urushidani, Tetsuro.

In: Journal of Toxicological Sciences, Vol. 31, No. 5, 12.2006, p. 449-469.

Research output: Contribution to journalArticle

Tamura, Kotaro ; Ono, Atsushi ; Miyagishima, Toshikazu ; Nagao, Taku ; Urushidani, Tetsuro. / Comparison of gene expression profiles among papilla, medulla and cortex in rat kidney. In: Journal of Toxicological Sciences. 2006 ; Vol. 31, No. 5. pp. 449-469.
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