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Results for “Gene expression analysis”

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At least 307 records · Page 17Linked to original sources
PubMed2005

Gene expression analysis and clinical diagnosis.

BACKGROUND: A new basis for diagnostic tests is being provided by the vast amount of data on gene expression that are now becoming available through large-scale measurement of mRNA abundance. The insights gained from these resources are most likely going to provide both a better basic understanding of disease mechanisms, and to identify molecular markers for more precise diagnoses and for prediction of prognosis and treatment response. METHODS: Some quantitative RT-PCR assays are utilized today for diagnosis of both malignant and non-malignant disease, but the use of gene expression measurements in clinical medicine can be expected to increase dramatically. CONCLUSIONS: There are important technical issues that must be adequately solved in order to obtain robust assays, such as standardized protocols with appropriate quality controls that ensure reliable data for the specific samples being analysed and good inter-laboratory reproducibility.

Biomarkers, Tumor↗
PubMed2003

Comprehensive gene expression analysis of peroxisome proliferator-treated immortalized hepatocytes: identification of peroxisome proliferator-activated receptor alpha-dependent growth regulatory genes.

Chemicals known as peroxisome proliferators (PPs) are the subject of intense study because of their ability to cause hepatocellular carcinoma in laboratory rodents. These chemicals act through a family of proteins termed the peroxisome proliferator-activated receptors (PPARs), in particular PPARalpha. It has become increasingly apparent that the role of the PPs in the development of cancer encompasses many different aspects of cell growth regulation. Immortalized hepatocytes from wild-type (PPARalpha(+/+)) and PPARalpha(-/-) mice were generated using a temperature-sensitive SV40 virus. Characterization of the murine SV40 hepatocytes (MuSH) generated from both genotypes (MuSHalpha(+/+), MuSHalpha(-/-)) show markers of differentiation such as albumin expression, but is devoid of Kupffer cell contamination. Hallmark PPARalpha-mediated responses such as induction of acyl-CoA oxidase mRNA by PPs are present in the MuSHalpha(+/+) but are absent in MuSHalpha(-/-) cells. In contrast to most cell culture systems, the wild-type MuSH hepatocytes retain the mitogenic activity of PPs, whereas the MuSHalpha(-/-) does not respond in this manner, thus making this cell culture system an ideal tool to examine growth regulatory gene expression affected by PPs. Microarray experiments performed on both cell types identified many genes in which regulation is dependent on the presence of PPARalpha, and these changes were verified with reverse transcriptase-PCR. Genes involved in carcinogenesis and control of the cell cycle that are regulated by PPs in a PPARalpha-dependent manner include ubiquitin COOH-terminal hydrolase 37 (also known as UCT-L5) and cyclin T1. These results show that MuSH cells reflect the biological properties of both the wild-type and PPARalpha-null animals and can be used to identify novel PPARalpha-regulated genes that could be involved in regulation of the cell cycle and carcinogenesis.

Animals↗
PubMed2004

A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells.

To understand how plant cell changes gene expression during cell division and after termination of cell division, we analyzed the change of gene expression during the growth of tobacco BY-2 cell lines using a cDNA microarray, which contained about 9,200 expression sequence tag fragments and corresponded to about 7,000 genes. We found that log phase cells predominantly expressed DNA/chromosome duplication gene homologs. In addition, many genes for basic transcription and translation machineries, as well as proteasomal genes, were up-regulated at the log phase. About half of the kinesin homolog genes, but not myosin homolog genes, were predominantly expressed at the dividing phase as well. In contrast, stationary phase cells expressed genes for many receptor kinases, signal transduction machineries and transcription factors. Several hundreds of genes showed differential expression after incubation of stationary phase cells with medium containing either salicylic acid or abscisic acid. These findings suggested that BY-2 cells at the stationary phase express genes for perceiving extracellular signals.

Base Sequence↗
PubMed2006

Cellular effect of high doses of silica-coated quantum dot profiled with high throughput gene expression analysis and high content cellomics measurements.

Quantum dots (Qdots) are now used extensively for labeling in biomedical research, and this use is predicted to grow because of their many advantages over alternative labeling methods. Uncoated Qdots made of core/shell CdSe/ZnS are toxic to cells because of the release of Cd2+ ions into the cellular environment. This problem has been partially overcome by coating Qdots with polymers, poly(ethylene glycol) (PEG), or other inert molecules. The most promising coating to date, for reducing toxicity, appears to be PEG. When PEG-coated silanized Qdots (PEG-silane-Qdots) are used to treat cells, toxicity is not observed, even at dosages above 10-20 nM, a concentration inducing death when cells are treated with polymer or mercaptoacid coated Qdots. Because of the importance of Qdots in current and future biomedical and clinical applications, we believe it is essential to more completely understand and verify this negative global response from cells treated with PEG-silane-Qdots. Consequently, we examined the molecular and cellular response of cells treated with two different dosages of PEG-silane-Qdots. Human fibroblasts were exposed to 8 and 80 nM of these Qdots, and both phenotypic as well as whole genome expression measurements were made. PEG-silane-Qdots did not induce any statistically significant cell cycle changes and minimal apoptosis/necrosis in lung fibroblasts (IMR-90) as measured by high content image analysis, regardless of the treatment dosage. A slight increase in apoptosis/necrosis was observed in treated human skin fibroblasts (HSF-42) at both the low and the high dosages. We performed genome-wide expression array analysis of HSF-42 exposed to doses 8 and 80 nM to link the global cell response to a molecular and genetic phenotype. We used a gene array containing approximately 22,000 total probe sets, containing 18,400 probe sets from known genes. Only approximately 50 genes (approximately 0.2% of all the genes tested) exhibited a statistically significant change in expression level of greater than 2-fold. Genes activated in treated cells included those involved in carbohydrate binding, intracellular vesicle formation, and cellular response to stress. Conversely, PEG-silane-Qdots induce a down-regulation of genes involved in controlling the M-phase progression of mitosis, spindle formation, and cytokinesis. Promoter analysis of these results reveals that expression changes may be attributed to the down-regulation of FOXM and BHLB2 transcription factors. Remarkably, PEG-silane-Qdots, unlike carbon nanotubes, do not activate genes indicative of a strong immune and inflammatory response or heavy-metal-related toxicity. The experimental evidence shows that CdSe/ZnS Qdots, if appropriately protected, induce negligible toxicity to the model cell system studied here, even when exposed to high dosages. This study indicates that PEG-coated silanized Qdots pose minimal impact to cells and are a very promising alternative to uncoated Qdots.

Cell Line↗
PubMed2006

Improved biplex quantitative real-time polymerase chain reaction with modified primers for gene expression analysis.

Stabilizing modified bases incorporated in primers allows the reduction of housekeeping gene primer concentration not possible with regular primers without sacrificing amplification efficiency. Low primer concentration allows coamplification of the most abundant housekeeping genes with very rare templates without mutual inhibition. Real-time polymerase chain reaction (PCR) coamplification of 18S ribosomal RNA with several genes of interest was used in this study with MGB Eclipse (Nanogen, San Diego, CA) hybridization probes. The results may be useful for high throughput gene expression studies as they simplify validation experiments.

Animals↗
PubMed2004

Exploratory differential gene expression analysis in microarray experiments with no or limited replication.

We describe an exploratory, data-oriented approach for identifying candidates for differential gene expression in cDNA microarray experiments in terms of alpha-outliers and outlier regions, using simultaneous tolerance intervals relative to the line of equivalence (Cy5 = Cy3). We demonstrate the improved performance of our approach over existing single-slide methods using public datasets and simulation studies.

Analysis of Variance↗
PubMed2005

Global gene expression analysis revealed an unsuspected deo operon under the control of molybdate sensor, ModE protein, in Escherichia coli.

ModE protein, a molybdate sensor/regulator, controls the transcription of genes coding for molybdate uptake (mod), molybdopterin synthesis (moa), molybdoenzymes nitrate reductase (nap) and dimethylsulfoxide reductase (dms), as well as fermentative dihydrogen production (fdhF and hyc) and respiratory nitrate reductase (narXL) in Escherichia coli. The catalytic product of a second protein, MoeA, is also required for molybdate-dependent positive regulation of hyc and nar operons. To explore the potential role of ModE and MoeA in the regulation of other E. coli genes, the global gene expression profile of a wild type and a modE, moeA double mutant grown in glucose-minimal medium under anaerobic conditions were compared. Expression of 67 genes was affected by the modE and moeA mutations (P value <0.01). Of these, 17 differed by at least 2-fold or higher. Fourteen genes were expressed at a higher level in the mutant (2.4- to 23.9-fold) (notably, mod-molybdate transport, deo-nucleoside catabolism and opp-oligopeptide transport operons) and dmsA and yli operon were expressed at a higher level in the wild type parent (2.6- to 5.7-fold). One of the unexpected findings was repression of the deo operon by ModE. This was confirmed by quantitative RT-PCR and by the analysis of a deoC-lacZ fusion. The deo promoter/operator region contains a putative ModE-consensus sequence centered at -35 in which the adenines are replaced by guanines (TGTGT-N7-TGTGT). The ModE protein did bind to the deo upstream DNA and shifted its electrophoretic mobility. Bioinformatics analysis of the E. coli genome for ModE-consensus motif (TATAT-N7-TAYAT) identified 21 additional genes/operons including the moa as potential targets for Mo-control. The physiological role of many of the genes identified solely by bioinformatics (19/21) is unknown. Expression levels of these genes were similar in the parent and the isogenic modE, moeA mutant when cultured anaerobically in glucose-minimal medium. This study identified additional targets, such as deo and opp, for the Mo-dependent control in E. coli.

Escherichia coli↗
PubMed2005

Searching QTL by gene expression: analysis of diabesity.

BACKGROUND: Recent developments in sequence databases provide the opportunity to relate the expression pattern of genes to their genomic position, thus creating a transcriptome map. Quantitative trait loci (QTL) are phenotypically-defined chromosomal regions that contribute to allelically variant biological traits, and by overlaying QTL on the transcriptome, the search for candidate genes becomes extremely focused. RESULTS: We used our novel data mining tool, ExQuest, to select genes within known diabesity QTL showing enriched expression in primary diabesity affected tissues. We then quantified transcripts in adipose, pancreas, and liver tissue from Tally Ho mice, a multigenic model for Type II diabetes (T2D), and from diabesity-resistant C57BL/6J controls. Analysis of the resulting quantitative PCR data using the Global Pattern Recognition analytical algorithm identified a number of genes whose expression is altered, and thus are novel candidates for diabesity QTL and/or pathways associated with diabesity. CONCLUSION: Transcription-based data mining of genes in QTL-limited intervals followed by efficient quantitative PCR methods is an effective strategy for identifying genes that may contribute to complex pathophysiological processes.

Algorithms↗
PubMed1999

Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG.

The massively parallel hybridization technologies by DNA chips and microarrays make it possible to monitor expression patterns of the whole set of genes in a genome under various conditions. The vast amount of data generated by such technologies necessitates the development of a new database management system that integrates expression data with other molecular biology databases and various analysis tools. We report here an extension of our KEGG (Kyoto Encyclopedia of Genes and Genomes) and DBGET/LinkDB systems for analyzing gene expression data in conjunction with pathway information and genomic information. It is now possible to make use of expression data for the reconstruction of pathways from the complete genome sequences.

Journal Article↗
PubMed2004

Gene expression analysis on biochemical networks using the Potts spin model.

MOTIVATION: Microarray technology allows us to profile the expression of a large subset or all genes of a cell. Biochemical research over the last three decades has elucidated an increasingly complete image of the metabolic architecture. For less complex organisms, such as Escherichia coli, the biochemical network has been described in much detail. Here, we investigate the clustering of such networks by applying gene expression data that define edge lengths in the network. RESULTS: The Potts spin model is used as a nearest neighbour based clustering algorithm to discover fragmentation of the network in mutants or in biological samples when treated with drugs. As an example, we tested our method with gene expression data from E.coli treated with tryptophan excess, starvation and trpyptophan repressor mutants. We observed fragmentation of the tryptophan biosynthesis pathway, which corresponds well to the commonly known regulatory response of the cells.

Algorithms↗
PubMed2004

Gene expression analysis of human renal biopsies: recent developments towards molecular diagnosis of kidney disease.

PURPOSE OF REVIEW: The analysis of renal tissue from kidney biopsies by histology, electron microscopy and immunohistology represents the current standards used to establish a specific diagnosis in nephrology. Recent progress in gene expression-based tissue analysis may provide fundamentally novel information in renal biopsy interpretation. In this review, progress towards the routine application of this approach is summarized. RECENT FINDINGS: Renal disease is characterized by closely interrelated mechanisms of inflammation, repair, scarring and atrophy affecting over 20 different intrinsic renal cell types. The renal biopsy sample represents a 'snapshot' of these dynamic processes. A central question for molecular diagnosis is whether specific gene expression patterns can adequately define segments of these disease processes. Can molecular markers be extracted as effectively as has been shown in oncology? Several studies have been able to correlate renal gene expression patterns with clinical parameters, renal histological findings and patient follow-up data. In small populations, molecular markers have been able to provide novel diagnostic, prognostic and differential therapeutic information beyond conventional histology. SUMMARY: A growing number of renal gene expression projects are generating targets for the integration of molecular approaches into kidney biopsy evaluation. If these molecular makers can pass rigorous testing for their diagnostic value, they should become an indispensable part of the management of the renal patient.

Biomarkers↗