Department of Physiology; Department of Pediatrics; Department of Dermatology; and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin

Correspondence: Mingyu Liang, M.B., Ph.D., Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226. E-mail:mliang@mcw.edu

Received 27 April 2004; Revised 9 July 2004; Re-revised 13 August 2004; Accepted 9 February 2005.

Abstract

Transcriptome analysis and kidney research: Toward systems biology. An enormous amount of data has been generated in kidney research using transcriptome analysis techniques. In this review article, we first describe briefly the principles and major characteristics of several of these techniques. We then summarize the progress in kidney research that has been made by using transcriptome analysis, emphasizing the experience gained and the lessons learned. Several technical issues regarding DNA microarray are highlighted because of the rapidly increased use of this technology. It appears clear from this brief survey that transcriptome analysis is an effective and important tool for question-driven exploratory science. To further enhance the power of this and other high throughput, as well as conventional approaches, in future studies of the kidney, we propose a multidimensional systems biology paradigm that integrates investigation at multiple levels of biologic regulation toward the goal of achieving a global understanding of physiology and pathophysiology.