ABSTRACT
Standard controls and best practice guidelines advance acceptance of data from research, preclinical and clinical laboratories by providing a means for evaluating data quality. The External RNA Controls Consortium (ERCC) is developing commonly agreed-upon and tested controls for use in expression assays, a true industry-wide standard control.
Subject(s)
Gene Expression Profiling/standards , Oligonucleotide Array Sequence Analysis/standards , RNA, Messenger/analysis , Animals , Guidelines as Topic , Humans , Mice , Quality Control , RatsABSTRACT
BACKGROUND: Previous studies from our laboratory have identified a novel mu opiate receptor micro(3), which is expressed in several different cell types and tissues including human vascular endothelial cells, leukocytes and neural tissues. This novel micro receptor is selective for the opiate alkaloid morphine, since this receptor does not bind other opioid peptides. MATERIAL/METHODS: This report details the acute affects of morphine exposure (1 microg/ml) to human leukocytes by analyzing gene expression using microarrays (Applied Biosystems). Robust estimation of the median fold change was used to identify candidates for significantly differentially expressed genes. An independent experiment using four same sample arrays was used to test the algorithm and to confirm the calculated percentage of falsely significant genes. RESULTS: Data obtained from this study demonstrate that acute morphine exposure differentially affected genes that are involved in immune function, signal transduction, cell adhesion, and apoptosis. CONCLUSIONS: Acute morphine exposure to human leukocytes results in specific and significant alterations in gene expression.
Subject(s)
Gene Expression Regulation/drug effects , Leukocytes/drug effects , Leukocytes/metabolism , Morphine/pharmacology , Algorithms , Gene Expression Profiling/statistics & numerical data , Humans , In Vitro Techniques , Interleukin-2/genetics , Oligonucleotide Array Sequence Analysis/statistics & numerical data , Receptors, Opioid, mu/metabolism , Signal Transduction/genetics , Tumor Necrosis Factor-alpha/geneticsABSTRACT
We aligned Incyte ESTs and publicly available sequences to the rat genome and analyzed rat chromosome 1q43-54, a region in which several quantitative trait loci (QTLs) have been identified, including renal disease, diabetes, hypertension, body weight, and encephalomyelitis. Within this region, which contains 255 Ensembl gene predictions, the aligned sequences clustered into 568 Incyte genes and gene fragments. Of the Incyte genes, 261 (46%) overlapped 184 (72%) of the Ensembl gene predictions, whereas 307 were unique to Incyte. The rat-to-human syntenic map displays rearrangement of this region on rat chr. 1 onto human chromosomes 9 and 10. The mapping of corresponding human disease phenotypes to either one of these chromosomes has allowed us to focus in on genes associated with disease phenotypes. As an example, we have used the syntenic information for the rat Rf-1 disease region and the orthologous human ESRD disease region to reduce the size of the original rat QTL to only 11.5 Mb. Using the syntenic information in combination with expression data from ESTs and microarrays, we have selected a set of 66 candidate disease genes for Rf-1. The combination of the results from these different analyses represents a powerful approach for narrowing the number of genes that could play a role in the development of complex diseases.
