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Topic: Expression profiling

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	Mayo Clinic: Gene expression profiling not quite perfected in predicting lung cancer prognosis
		Researchers caution that the science of gene expression profiling, in which scientists examine the genetic signature of a cell, is in its infancy, particularly in lung cancer.
		Yang, a researcher with Mayo Clinic's Department of Health Sciences, said that while gene expression profiling has been successfully used to classify various tumors and assess tumor stage, metastasis and patient survival rates, the evidence suggests that gene-based prediction for lung cancer is not yet entirely dependable.
		Current analytical algorithms favor genes at high expression or genes highly differentially expressed, most of which are related to tumor differentiation and may not correlate with clinical outcomes; conversely, genes expressed at low levels or in a subtle difference are often overlooked, which may be quite relevant biologically to clinical questions.
	www.eurekalert.org /pub_releases/2006-11/mc-mcg111506.php (579 words)

	Gene expression - Wikipedia, the free encyclopedia
		Gene expression is a multi-step process that begins with transcription and translation and is followed by folding, post-translational modification and targeting.
		Indirectly, the expression of particular genes may be assessed with DNA microarray technology, which can provide a rough measure of the cellular concentration of different mRNAs; often thousands at a time.
		Nonetheless, bacterial expression has the advantage of easily producing large amounts of protein, which is required for X-ray crystallography or NMR experiments for structure determination.
	en.wikipedia.org /wiki/Gene_expression (683 words)

	Gene Expression Profiling
		The correlation of transcript profiles, probe clustering, and expression patterns in a particular tissue or developmental stage may help to assign biological relevance to many of the unknown genes.
		SAGE analyses have already been used to study gene expression in plant systems.12-13 Among the high-throughput, comprehensive technological methods used to analyze transcript expression levels, array-based hybridization and SAGE are currently the most common approaches.
		In a recent comparison of SAGE and array-based technologies, the two methods correlated quite well in both absolute expression analyses and comparative analyses during differentiation.14 The correlation was better for genes with higher expression levels and greater changes in expression.
	www.noble.org /medicago/GEP.html (778 words)

	Gene expression profiling of pediatric acute myelogenous leukemia -- Ross et al. 104 (12): 3679 -- Blood
		Expression profiles of the diagnostic leukemic blasts from 130 cases of pediatric AML were obtained using the U133A Affymetrix microarray.
		Gene expression profiles of pediatric acute leukemia with MLL chimeric fusion genes.
		Expression profiles of acute lymphoblastic and myeloblastic leukemias with ALL-1 rearrangements.
	www.bloodjournal.org /cgi/content/full/104/12/3679 (6950 words)

	Expression profiling using cDNA microarrays - Nature Genetics (Site not responding. Last check: 2007-11-06)
		The accumulation of expression data has yet to reach the point at which it is possible to speak of expression motifs, but it does suggest that this is a plausible outcome of the approach
		Comparison of expression profiles will undoubtedly provide useful insights into the molecular pathogenesis of a variety of diseases (ref. 29; see also, page 48 of this issue (ref. 30)).
		Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays.
	www.nature.com /cgi-taf/DynaPage.taf?file=/ng/journal/v21/n1s/full/ng0199supp_10.html (3994 words)

	BioMed Central \| Full text \| Domain-oriented functional analysis based on expression profiling
		Expression monitoring on a genome-wide scale was first successfully demonstrated in budding yeast [1,13,14].
		Whole-genome expression profiles provide a rich source of information on protein function, protein-protein interactions, and gene pathways, and have been compared with data sets describing transcription factor binding sites, protein families, protein-protein interactions, and protein abundance [15-22] mainly in budding yeast.
		In order to analyze the expression profile for each Pfam family, we calculated the Family Regulation Ratio (FRR) for each Pfam family as the percentage of its members which were "regulated" in a pair-wise comparison and assigned the ratio to the Pfam ID for this probe pair.
	www.biomedcentral.com /1471-2164/3/32 (4415 words)

	Gene expression profiling of multiple myeloma reveals molecular portraits in relation to the pathogenesis of the ...
		The normalized expression value for each gene is depicted according to the scale at the bottom; red indicates expression levels greater than the median, and green indicates levels less than the median (–2 to 2 in log base 2 units).
		A pseudocolor representation of gene expression is shown according to the scale at the bottom; red indicates expression levels greater than the median, and green indicates levels less than the median.
		Molecular classification of cutaneous malignant melanoma by gene expression profiling.
	www.bloodjournal.org /cgi/content/full/101/12/4998 (5419 words)

	NSF Arabidopsis 2010: Expression Profiling of Plant Disease Resistance Pathways Project
		This database will be developed during the next four years and will contain standardized experimental procedures for analyzing host defense responses, a list of all the pathogenesis-related mutants and their phenotypes, a list of defense-related genes with links to various sequence databases, and expression profiles of different plant-pathogen interactions and different defense-related mutants.
		TFs are key switches that control plant defense responses against pathogens, and expression profiling using gene chip (microarray) is the most powerful genomics approach available for high through-put analysis of transcriptional events.
		In Aim 1, profiling will identify candidate TFs in understudied defense pathways, including those induced by the so-called "PAMP" molecules which are commonly associated with pathogens of plants as well as animals.
	ausubellab.mgh.harvard.edu /nsf2010/index.jsp (736 words)

	Genome Biology \| Full text \| Expression profiling in reference bacteria: dreams and reality
		Profiling of gene expression in bacteria is now being used to uncover unknown genes expressed in particular genetic backgrounds or environmental conditions.
		Transcription expression profiling can be used to investigate either the transcriptome (the totality of genes transcribed) or the proteome (the totality of the proteins produced) of a bacterium.
		Their third important contribution was to show convincingly that the popular tendency to equate the magnitude of the fold-difference between the expression levels of a gene obtained under two experimental conditions with the accuracy of those measurements was very misleading.
	genomebiology.com /2000/1/4/reviews/1024 (3645 words)

	Expression Profiling of Mammalian Male Meiosis and Gametogenesis Identifies Novel Candidate Genes for Roles in the ...
		Expression Profiling of Mammalian Male Meiosis and Gametogenesis Identifies Novel Candidate Genes for Roles in the Regulation of Fertility -- Schlecht et al.
		Expression signal intensities are shown in red and blue indicating high and low expression, respectively.
		Gromoll, J., Wessels, J., Rosiepen, G., Brinkworth, M.H., and Weinbauer, G.F. Expression of mitotic cyclin B1 is not confined to proliferating cells in the rat testis.
	www.molbiolcell.org /cgi/content/full/15/3/1031 (7254 words)

	Journal of Translational Medicine \| Full text \| Gene expression profiling of cutaneous wound healing
		HIF is a nuclear transcription factor whose expression is increased in endothelial cells and that stimulates the expression of VEGF and hence angiogenesis [1].
		To determine the polarization of the macrophage activation, all macrophage genes whose expression changed were selected, (see additional file 2) and supervised hierarchical clustering was used to analyze the expression of these M1 and M2 macrophage genes in the pre- and post-wound samples from all 14 subjects.
		The expression of methallothioneins is increased in metabolically active and proliferating cells of the dermis.
	www.translational-medicine.com /content/5/1/11 (4618 words)

	Breast Cancer Research \| Full text \| Predicting a local recurrence after breast-conserving therapy by gene expression ...
		This analysis is based on previously reported gene expression profiles of tumors from a series of 295 stage I and II breast cancer patients treated at the Netherlands Cancer Institute between 1984 and 1995 [23].
		The microarray data for analysis of the 70-gene prognosis profile were obtained with the use of the same 25,000-element oligonucleotide array; the correlation coefficient of the expression of these 70 genes with the good prognosis profile was calculated as reported previously [22].
		The wound-response gene expression signature is a characteristic pattern of expression of a set of genes that have been identified as being induced or repressed in response to bovine serum, a surrogate wound environment [30,34].
	breast-cancer-research.com /content/8/5/R62 (6046 words)

	Sequential gene expression profiling in lung transplant recipients with chronic rejection.
		Using microarray technology, we identified and compared gene expression profiling in lung transplant recipients with and without chronic rejection, and follow sequential expression of genes differentially expressed between the two groups.
		Gene expression profiling was obtained from hybridizing BAL fluid cell RNA to a 96-gene microarray.
		Temporal expression of the significant genes demonstrated a change in their levels at the onset of chronic rejection, with normalization to prerejection levels as rejection continued.
	lungtransplant.researchtoday.net /archive/2/9/255.htm (311 words)

	Gene Expression Profiling of Embryo-Derived Stem Cells Reveals Candidate Genes Associated With Pluripotency and Lineage ...
		(B) Expression patterns of Esg-1 and Oct3/4 were examined in unfertilized eggs (UN; 278 eggs), fertilized eggs (1; 248 zygotes), and preimplantation embryos at stages of 2-, 4-, and 8-cells (289, 312, and 181 embryos, respectively), morula (M; 144 embryos), and blastocyst (B; 175 embryos).
		Christians, E., Campion, E., Thompson, E.M., and Renard, J.P. Expression of the HSP 70.1 gene, a landmark of early zygotic activity in the mouse embryo, is restricted to the first burst of transcription.
		Niwa, H., Miyazaki, J., and Smith, A.G. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells.
	www.genome.org /cgi/content/full/12/12/1921 (6112 words)

	High-Density Microarray-Mediated Gene Expression Profiling of Escherichia coli -- Wei et al. 183 (2): 545 -- The ... (Site not responding. Last check: 2007-11-06)
		High-Density Microarray-Mediated Gene Expression Profiling of Escherichia coli
		Basal expression levels expressed as normalized equivalent readings were plotted on the ordinate, and induced levels, also normalized equivalent readings, were plotted on the abscissa.
		Expression of 766, 1,030, and 1,776 genes was not detected under the three respective conditions.
	jb.asm.org /cgi/content/full/183/2/545 (7847 words)

	BioMed Central \| Full text \| Gene expression profiling of chicken primordial germ cell ESTs
		However, digital gene expression profiling using the Audic's test showed that there were 2 genes expressed significantly with higher number of transcripts in PGCs compared with the embryonic gonads set.
		Significance test of gene expression profiles between a pair of the cDNA libraries was performed using Audic's [14] test.
		Expression comparison of the gene was performed with the number of reads of the gene of two datasets.
	www.biomedcentral.com /1471-2164/7/220 (3832 words)

	Pharmaceutical Gene expression & protein expression glossary
		Gene expression profiling has the potential to be used for differentiating types of cancer (and other diseases) that appear identical to pathologists today.
		A shift in gene expression that occurs when cells are transferred from a rich medium to a poorer medium, or when cells in a rich medium grow and deplete their medium of nutrients.
		Expression Profiling for Compound Characterization and Prioritization, Sept. 26-28, 2005, Philadelphia PA Refers to the expression values for a single gene across many experimental conditions, or for many genes under a single condition.
	www.genomicglossaries.com /content/ex_bio.asp (7459 words)

	High-Throughput RNA Isolation Technologies. New Tools for High-Resolution Gene Expression Profiling in Plant Systems -- ...
		in multicellular organisms is the heterogeneity of gene expression.
		Leonhardt N, Kwak JM, Robert N, Waner D, Leonhardt G, Schroeder JI (2004) Microarray expression analysis of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2c mutant.
		Milioni D, Sado P-E, Stacey NJ, Roberts K, McCann MC (2002) Early gene expression associated with the commitment and differentiation of a plant tracheary element is revealed by cDNA-amplified fragment length polymorphism analysis.
	www.plantphysiol.org /cgi/content/full/138/2/585 (3051 words)

	Genencor: Transcription Profiling (Site not responding. Last check: 2007-11-06)
		Expression or transcript profiling is an important component of Functional Genomics.
		Our transcript profiling data is used to determine which genes are expressed under different fermentation conditions, and how the manipulation of a particular metabolic or regulatory pathway can have global effects on the growth of the organism and its protein production/secretion capabilities.
		We have used transcript profiling information gained from the Trichoderma reesei genome for our NREL project to help identify novel genes involved in cellulose degradation, in turn aiding our understanding of regulation of cellulase gene expression and aiding in optimizing fermentation conditions.
	www.genencor.com /wt/gcor/gene_transcript (357 words)

	Microarray Analysis and Gene Expression Profiling
		Gene expression profiling or microarray analysis has enabled the measurement of thousands of genes in a single RNA sample.
		There are a variety of microarray platforms that have been developed to accomplish this and the basic idea for each is simple: a glass slide or membrane is spotted or "arrayed" with DNA fragments or oligonucleotides that represent specific gene coding regions.
		A number of issues must be addressed before establishing a microarray platform and beginning expression profiling studies, in particular, the overall cost.
	www.microarrayworld.com (632 words)

	Gene Expression Profiling May Help Distinguish Types of Brain Tumors
		The identified patterns tend to be strongly associated with a specific type of cancer and/or specific characteristics of the cancer, such as its aggressiveness or response to therapy.
		The researchers evaluated the expression of 2,600 genes in an attempt to identify patterns specific to each type of tumor.
		Microarray-based gene expression profiling of benign, atypical and anaplastic meningiomas identifies novel genes associated with meningioma progression.
	patient.cancerconsultants.com /news.aspx?id=33384 (540 words)

	NSF Potato Functional Genomics
		To increase the available data on the Solanaceae, TIGR has established a gene expression profiling service for the Solanaceae community.
		All expression data from the expression profiling service will be made public after 60 days via the TIGR Solanaceae Gene Expression Profile database.
		Note: the Expression Profiling Service program has ended and we are no longer accepting any new applications for this service.
	www.tigr.org /tdb/potato/profiling_service2.shtml (871 words)

	Affymetrix GeneChip Genotyping Services from Expression Analysis
		Expression Analysis uses the high density Affymetrix Mapping arrays to assay as many as 500,000 SNPs from only 250 ng of genomic DNA per array.
		Expression Analysis was one of the first service providers to offer testing on both the 100K and 500K Array Sets.
		Expression Analysis scientists work closely with both Affymetrix and our clients to optimize genotyping protocols resulting in increased call rates.
	www.expressionanalysis.com /genotyping.html (494 words)

	CHI, Cambridge Healthtech Institute
		Following lead selection, we use gene expression microarrays to identify a set of biomarkers that describes the most desired effects of the compound series, and use this core gene set to drive chemical optimization toward the identification of a development candidate.
		Additionally, gene expression biomarker sets are used in in vivo experiments that accelerate pharmacologic optimization and establish clinical biomarkers to 1) guide dose escalation 2) correlate patient responses with pre-clinical efficacy results, and 3) enrich for responsive patients.
		In contrast, gene expression profile analysis could provide a physiological, as well as a thorough and unbiased snapshot of the gene expression changes resulting from compound treatment, and thus, a more accurate assessment of a compound selectivity in cells.
	www.healthtech.com /2005/bmks/cpf.asp (857 words)

	Gene expression profiling
		Knowledge of the changes in gene expression typical for certain types and stages of tumors can give insight into the molecular changes involved in disease development and progression and provide molecular markers for diagnosis and prognosis.
		We compare the gene expression data with clinical, histological, and cytogenetic data in order to find new (sub)classes of tumors and prognostic markers.
		Furthermore, the gene expression data are utilized to analyze the effects of the corresponding proteins on biological processes (Functional Profiling Group: Dorit Arlt, Stefan Wiemann; Disease Projects Group: Jan Mollenhauer, Sabine Klauck).
	www.dkfz.de /en/mga/Groups/ExpressionProfiling.html (198 words)

	NIH Guide: GENE EXPRESSION PROFILING IN THE NERVOUS SYSTEM
		The determination of the profile of genes expressed in various brain cell types during development and aging, as well as alterations in gene expression patterns during pathophysiological states or in response to external influences, will provide valuable information that will contribute to a greater understanding of nervous system functioning.
		DNA microarray technologies offer the ability to monitor simultaneously the expression patterns of large numbers of genes that are relevant to nearly every aspect of neuroscience research.
		In addition, the RFA number and title, “MH-00-002: Gene Expression Profiling in the Nervous System,” must be typed on line 2 of the face page of the application form and the YES box must be marked.
	grants.nih.gov /grants/guide/rfa-files/RFA-MH-00-002.html (3815 words)

	Gene Expression Profiling of Cultured Human Bronchial Epithelial and Lung Carcinoma Cells -- Hellmann et al. 61 (1): ... (Site not responding. Last check: 2007-11-06)
		Gene Expression Profiling of Cultured Human Bronchial Epithelial and Lung Carcinoma Cells -- Hellmann et al.
		Gene Expression Profiling of Cultured Human Bronchial Epithelial and Lung Carcinoma Cells
		Gene expression profiles were compared within and among
	toxsci.oxfordjournals.org /cgi/content/abstract/61/1/154 (429 words)

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