Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives

• Published in: The Plant journal : for cell and molecular biology 2006-02, Vol.45 (4), p.630-650
• Main Authors: Clarke, Joseph D., Zhu, Tong
• Format: Article
• Language: English
• Subjects: Analytical, structural and metabolic biochemistry; Biological and medical sciences; Blotting, Northern; DNA Probes; functional genomics; Fundamental and applied biological sciences. Psychology; gene expression; General aspects, investigation methods; microarray; Oligonucleotide Array Sequence Analysis; Plants - genetics; Proteins; Reverse Transcriptase Polymerase Chain Reaction; RNA, Messenger - genetics; systems biology; transcriptome
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/j.1365-313X.2006.02668.x

Summary DNA microarrays have been used to characterize plant transcriptomes to answer various biological questions. While many studies have provided significant insights, there has been great debate about the general reliability of the technology and data analysis. When compared to well‐established transcript analysis technologies, such as RNA blot analysis or quantitative reverse transcription‐PCR, discrepancies have frequently been observed. The reasons for these discrepancies often relate to the technical and experimental systems. This review‐tutorial addresses common problems in microarray analysis and describes: (i) methods to maximize extraction of valuable biological information from the vast amount of microarray data and (ii) approaches to balance resource availability with high scientific standards and technological innovation with peer acceptability.