Cross-platform comparison of SYBR® Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study

<p>Abstract</p> <p>Background</p> <p>The MicroArray Quality Control (MAQC) project evaluated the inter- and intra-platform reproducibility of seven microarray platforms and three quantitative gene expression assays in profiling the expression of two commercially available Reference RNA samples (<b><it>Nat Biotechnol </it></b>24:1115-22, 2006). The tested microarrays were the platforms from Affymetrix, Agilent Technologies, Applied Biosystems, GE Healthcare, Illumina, Eppendorf and the National Cancer Institute, and quantitative gene expression assays included TaqMan^®Gene Expression PCR Assay, Standardized (Sta) <it>RT</it>-PCR™ and QuantiGene^®. The data showed great consistency in gene expression measurements across different microarray platforms, different technologies and test sites. However, SYBR^®Green real-time PCR, another common technique utilized by half of all real-time PCR users for gene expression measurement, was not addressed in the MAQC study. In the present study, we compared the performance of SYBR Green PCR with TaqMan PCR, microarrays and other quantitative technologies using the same two Reference RNA samples as the MAQC project. We assessed SYBR Green real-time PCR using commercially available RT²Profiler™ PCR Arrays from SuperArray, containing primer pairs that have been experimentally validated to ensure gene-specificity and high amplification efficiency.</p> <p>Results</p> <p>The SYBR Green PCR Arrays exhibit good reproducibility among different users, PCR instruments and test sites. In addition, the SYBR Green PCR Arrays have the highest concordance with TaqMan PCR, and a high level of concordance with other quantitative methods and microarrays that were evaluated in this study in terms of fold-change correlation and overlap of lists of differentially expressed genes.</p> <p>Conclusion</p> <p>These data demonstrate that SYBR Green real-time PCR delivers highly comparable results in gene expression measurement with TaqMan PCR and other high-density microarrays.</p

Genome-wide estimation of gender differences in the gene expression of human livers: Statistical design and analysis

BACKGROUND: Gender differences in gene expression were estimated in liver samples from 9 males and 9 females. The study tested 31,110 genes for a gender difference using a design that adjusted for sources of variation associated with cDNA arrays, normalization, hybridizations and processing conditions. RESULTS: The genes were split into 2,800 that were clearly expressed (expressed genes) and 28,310 that had expression levels in the background range (not expressed genes). The distribution of p-values from the 'not expressed' group was consistent with no gender differences. The distribution of p-values from the 'expressed' group suggested that 8 % of these genes differed by gender, but the estimated fold-changes (expression in males / expression in females) were small. The largest observed fold-change was 1.55. The 95 % confidence bounds on the estimated fold-changes were less than 1.4 fold for 79.3 %, and few (1.1%) exceed 2-fold. CONCLUSION: Observed gender differences in gene expression were small. When selecting genes with gender differences based upon their p-values, false discovery rates exceed 80 % for any set of genes, essentially making it impossible to identify any specific genes with a gender difference

Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor α agonists

BACKGROUND: Fibrates are a unique hypolipidemic drugs that lower plasma triglyceride and cholesterol levels through their action as peroxisome proliferator-activated receptor alpha (PPARα) agonists. The activation of PPARα leads to a cascade of events that result in the pharmacological (hypolipidemic) and adverse (carcinogenic) effects in rodent liver. RESULTS: To understand the molecular mechanisms responsible for the pleiotropic effects of PPARα agonists, we treated mouse primary hepatocytes with three PPARα agonists (bezafibrate, fenofibrate, and WY-14,643) at multiple concentrations (0, 10, 30, and 100 μM) for 24 hours. When primary hepatocytes were exposed to these agents, transactivation of PPARα was elevated as measured by luciferase assay. Global gene expression profiles in response to PPARα agonists were obtained by microarray analysis. Among differentially expressed genes (DEGs), there were 4, 8, and 21 genes commonly regulated by bezafibrate, fenofibrate, and WY-14,643 treatments across 3 doses, respectively, in a dose-dependent manner. Treatments with 100 μM of bezafibrate, fenofibrate, and WY-14,643 resulted in 151, 149, and 145 genes altered, respectively. Among them, 121 genes were commonly regulated by at least two drugs. Many genes are involved in fatty acid metabolism including oxidative reaction. Some of the gene changes were associated with production of reactive oxygen species, cell proliferation of peroxisomes, and hepatic disorders. In addition, 11 genes related to the development of liver cancer were observed. CONCLUSION: Our results suggest that treatment of PPARα agonists results in the production of oxidative stress and increased peroxisome proliferation, thus providing a better understanding of mechanisms underlying PPARα agonist-induced hepatic disorders and hepatocarcinomas

Genomic analysis of microRNA time-course expression in liver of mice treated with genotoxic carcinogen N-ethyl-N-nitrosourea

<p>Abstract</p> <p>Background</p> <p>Dysregulated expression of microRNAs (miRNAs) has been previously observed in human cancer tissues and shown promise in defining tumor status. However, there is little information as to if or when expression changes of miRNAs occur in normal tissues after carcinogen exposure.</p> <p>Results</p> <p>To explore the possible time-course changes of miRNA expression induced by a carcinogen, we treated mice with one dose of 120 mg/kg <it>N</it>-ethyl-<it>N</it>-nitrosourea (ENU), a model genotoxic carcinogen, and vehicle control. The miRNA expression profiles were assessed in the mouse livers in a time-course design. miRNAs were isolated from the livers at days 1, 3, 7, 15, 30 and 120 after the treatment and their expression was determined using a miRNA PCR Array. Principal component analysis of the miRNA expression profiles showed that miRNA expression at post-treatment days (PTDs) 7 and 15 were different from those at the other time points and the control. The number of differentially expressed miRNAs (DEMs) changed over time (3, 5, 14, 32, 5 and 5 at PTDs 1, 3, 7, 15, 30 and 120, respectively). The magnitude of the expression change varied with time with the highest changes at PTDs 7 or 15 for most of the DEMs. In silico functional analysis of the DEMs at PTDs 7 and 15 indicated that the major functions of these ENU-induced DEMs were associated with DNA damage, DNA repair, apoptosis and other processes related to carcinogenesis.</p> <p>Conclusion</p> <p>Our results showed that many miRNAs changed their expression to respond the exposure of the genotoxic carcinogen ENU and the number and magnitude of the changes were highest at PTDs 7 to 15. Thus, one to two weeks after the exposure is the best time for miRNA expression sampling.</p

Species traits of critically endangered species of the Czech Republic.

<p><b>Copyright information:</b></p><p>Taken from "Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver"</p><p>http://www.biomedcentral.com/1471-2105/8/S7/S22</p><p>BMC Bioinformatics 2007;8(Suppl 7):S22-S22.</p><p>Published online 1 Nov 2007</p><p>PMCID:PMC2099491.</p><p></p>ltered by both riddelliine and comfrey

Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver-2

<p><b>Copyright information:</b></p><p>Taken from "Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver"</p><p>http://www.biomedcentral.com/1471-2105/8/S7/S22</p><p>BMC Bioinformatics 2007;8(Suppl 7):S22-S22.</p><p>Published online 1 Nov 2007</p><p>PMCID:PMC2099491.</p><p></p> (up or down) and the -value was less than 0.01 in comparison to the control group. The color in green refers to the number of genes whose expressions were significantly altered by both comfrey and riddelliine

Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver-8

<p><b>Copyright information:</b></p><p>Taken from "Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver"</p><p>http://www.biomedcentral.com/1471-2105/8/S7/S22</p><p>BMC Bioinformatics 2007;8(Suppl 7):S22-S22.</p><p>Published online 1 Nov 2007</p><p>PMCID:PMC2099491.</p><p></p> (up or down) and the -value was less than 0.01 in comparison to the control group. The color in green refers to the number of genes whose expressions were significantly altered by both comfrey and riddelliine

Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver-5

<p><b>Copyright information:</b></p><p>Taken from "Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver"</p><p>http://www.biomedcentral.com/1471-2105/8/S7/S22</p><p>BMC Bioinformatics 2007;8(Suppl 7):S22-S22.</p><p>Published online 1 Nov 2007</p><p>PMCID:PMC2099491.</p><p></p>mbol means regulated in same direction, and red symbol means regulated in opposite direction

Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver-3

<p><b>Copyright information:</b></p><p>Taken from "Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver"</p><p>http://www.biomedcentral.com/1471-2105/8/S7/S22</p><p>BMC Bioinformatics 2007;8(Suppl 7):S22-S22.</p><p>Published online 1 Nov 2007</p><p>PMCID:PMC2099491.</p><p></p