Gene array analysis and the liver

Abstract

Functional genomics methods promise a previously unparalleled high‐throughput examination of intrahepatic gene expression. Profiling transcriptomes as well as examining the coordinate expression of many genes in diverse pathobiologic pathways is now pssible with techniques such as gene array analysis. However, the nature of the hepatic transcriptome, limitations of the functional genomics methokologies used, and analysis of the data generated are often poorly understood. Further, the use of replicates during analysis and the downstream confirmation of results using a supplemental methokology are important but frequently neglected aspects of experimenta design. This review presents an overview of functional genomics methodoogies in the organ‐specific context of studying intrahepatic gene expression. The focus of the review is the most widely used functional genomic methodology, gene array analysis. The nature of the hepatic transcriptome is discussed, together with a summary of gene array analysis methodologies. Analysis of data generated by gene array analysis, determination of intrahepatic cellular origin of transcript expression, and studies of intrahepatic gene expression using gene array analysis are also reviewed. Finally, the importance of a coordinate experimental approach examining both liver protein and mRNA expression is presented. (HEPATOLOGY 2002;36: 1313‐1325).

Intrahepatic gene expression in human alcoholic hepatitis

“…The predominance of this category of genes has also been reported in other forms of liver cirrhosis [12,13,19]. When taken together, these are the first studies to permit a comparison between gene expression profiles of early stage ALD, AH and endstage ALD.…”

Compendium of gene expression profiles comprising a baseline model of the human liver drug metabolism transcriptome

“…Similar microarraybased approaches to hepatic gene expression include the examination of the expression of 4043 genes in liver from five human donors (Yano et al 2001) and tissue-specific expression patterns in 23 040 genes in 25 human adults across 29 tissues (Saito-Hisaminato et al 2002). Some of the challenges arising in the earliest microarray-based assessments of the hepatic transcriptome have been highlighted by Shackel et al (2002).…”

Large-scale gene profiling of the liver in a mouse model of chronic, intragastric ethanol infusion

“…This technology has already been used in a number of studies in hepatology and provided important information [18 -22] (for a review see also Ref. [23]). Profiling of gene expression in alcoholic liver disease will provide further insights into disease mechanisms and will open new avenues for discovery of novel therapeutic means.…”