gene expression based high throughput screening

... mission The desired screening of thousands of candidate genes would require many person years without automation Relegating this task to a fully automated high- throughput screening system offers ... these regions can be generated A naive complete high- resolution scanning is out of the question due to the tight time constraints of a high- throughput system Therefore, the screening is divided ... de-novo discovery of genes affecting the barley/powdery mildew interaction Conclusion The described high- throughput screening system enables a large-scale analysis of candidate genes regarding the...

Ngày tải lên: 12/08/2014, 05:20

... for high- throughput screening PDGFR/ERK activation signature for high- throughput screening (a) Genes whose expression is correlated with ERK activation by PDGFR Genes (in rows) sorted by their expression ... in the high- throughput screen Figure Hit compounds that passed hit selection criteria in the high- throughput screen (a) Hit compounds identified in the screen (b) High- throughput screen expression ... Colavito SA, O'Malley S, Stockwell BR, Golub TR: Gene expression- based high- throughput screening( GEHTS) and application to leukemia differentiation Nat Genet 2004, 36:257-263 Hieronymus H, Lamb J,...

Ngày tải lên: 14/08/2014, 08:20

... for high throughput screening of G protein-coupled receptors J Biomol Screening 5(3), 159–167 14 Allen, M., Reeves, J., and Mellor, G (2000) High throughput fluorescence polarization: a homogeneous ... (1996) FLIPR: a new instrument for accurate, high throughput optical screening J Biomol Screen 1, 75 – Hertzberg, R P., and Pope, A J (2000) High throughput screening: new technology for the 21st century ... Lutz, M.W., Menius, J.A., et al (1996) Experimental design for high- throughput screening Drug Discov Today 1, 277 – 286 High Throughput Screening Assays 29 15 Taylor, P., Stewart, F., et al (2000)...

Ngày tải lên: 11/04/2014, 09:46

... overlapping transcriptional responses are generated by TGFβ stimulation in different tissues in different species In general, the expressions of 5–10% genes in the genome are affected upon TGFβ ... in gliomas to identify gene signatures that have the power to predict survival and subclasses of gliomas that represent distinct prognostic groups [25-27] Gene expression- based classification of ... oligoastrocytoma (Mix) The mean expression level of SERPINE1 is 6.1-fold higher in glioblastoma compared to anstrocytoma, 5.3-fold higher compared to mixed glioma and 1.9-folder higher compared to oligodendroglioma...

Ngày tải lên: 18/06/2014, 15:20

... of screening assays in cell lines that can simultaneously support virus replication and be responsive to measures of inhibition of virus replication are a priority Cell -based high- throughput screening ... studies reported here was to establish a cell -based screening assay that could identify compounds that inhibit virus replication by inducing antiviral gene expression pathways Although the assay could ... and changes in reporter gene expression in engineered cell lines to measure antiviral activity [5-8] For example, a dual replicon assay system that combined reporter gene assays and FRET was...

Ngày tải lên: 20/06/2014, 01:20

... GGI: GENE7 0: High risk High risk High risk High risk GENE7 6: High risk GENIUS: High risk Prediction Id: VDXIGRU_171558 Age: 35 years Tumor size: 3.2cm Grade ER- (IHC) Node- (c) High risk High ... score by gene expression - High proliferative tumor with low risk predicted by HER2+ subtype signature (e) AOL: NPI: GGI: Outcome High risk High risk High risk GENE7 0: High risk GENE7 6: High risk ... Low GENIUS Low / NPI High GENIUS High / NPI Low GENIUS High / NPI High 0.0 0.0 No At Risk GENIUS Low / AOL Low GENIUS Low / AOL High GENIUS High / AOL Low GENIUS High / AOL High 0.4 Probability...

Ngày tải lên: 09/08/2014, 20:21

... first generation molecular markers, such as RFLPs (Restriction Fragment Length Polymorphisms) and RAPDs (Random Amplified Polymorphic DNAs), SNPs can be detected through non-gel -based high- throughput ... eSNPs as a potential source for high- throughput genotyping methods Herein we report a successful application of the SNPlex genotyping system, which provided 563 new SNP -based markers anchoring the ... genotyping system application in higher plants, which allowed the development of markers anchoring the grapevine genome To date, a few low- and mid -throughput methods based on SSCP and minisequencing...

Ngày tải lên: 12/08/2014, 05:20

... NFI abrogated GIS-driven gene expression Mutation or deletion of the κB-consensus motif in this regulatory sequence reduced p53-RELA-mediated luciferase reporter gene expression by 50% and 30%, ... complex may control gene expression program in heart failure Understanding the way that different DNA binding proteins interact with DNA regulatory elements and modulate gene expression will provide ... 10.1186/gm158 Cite this article as: Choy et al., High- throughput sequencing identifies STAT3 as the DNA-associated factor for p53-NF-?B-complex-dependent gene expression in human heart failure Genome...

Ngày tải lên: 11/08/2014, 12:20

... of gene expression- based applications that have the potential to be transforming, particularly in the area of small molecule screening Highthroughput small molecule screens based on gene expression ... Colavito SA, O'Malley S, Stockwell BR, Golub TR: Gene expression- based high- throughput screening (GEHTS) and application to leukemia differentiation Nat Genet 2004, 36:257-263 Yang L, Tran DK, Wang ... Zhang B, Shen R, et al.: A versatile assay for highthroughput gene expression profiling on universal array matrices Genome Res 2004, 14:878-885 Gene Expression Omnibus [http://www.ncbi.nlm.nih.gov/geo/]...

Ngày tải lên: 14/08/2014, 16:21

... KEGGanim: pathway animations for high- throughput data Bioinformatics 24, 588–590 Antonov AV & Mewes HW (2006) Complex functionality of gene groups identified from high- throughput data J Mol Biol 363, ... complex functionality of gene groups identified from highthroughput data Nucleic Acids Res 36, W347–W351, doi:10.1093/nar/gkn239 Antonov AV & Mewes HW (2008) Complex phylogenetic profiling reveals ... Ostermeier GC & Krawetz SA (2002) Profiling gene expression using onto-express Genomics 79, 266–270 Khatri P & Draghici S (2005) Ontological analysis of gene expression data: current tools, limitations,...

Ngày tải lên: 16/03/2014, 01:20

... the introduction of H1, H2 and H3 hemagglutinin (HA) gene segments from an avian virus source [5] early after infection This affords higher throughput with excellent signal/noise ratios, providing ... effective Unfortunately these latter viral inhibition assays are usually not suited to high throughput screening (HTS) In this report we describe modifications of the standard virus neutralization ... activity has previously been used to quantify virus [16] For the purpose of developing a high throughput screening assay, we needed to show that NA activity is readily measured in virus preparations...

Ngày tải lên: 20/06/2014, 01:20

... clustering based on expression profile shape (or trajectory) rather than absolute levels Kim et al [7] show that genes with similar function often exhibit similarity in signal shape even though the expression ... apart Therefore, expression shape is a more important indication of similar gene functions than expression magnitude The same clustering methods mentioned above can be used based on shape similarity ... of genes with similar functions; that is, coregulated genes using EURASIP Journal on Bioinformatics and Systems Biology time-series microarray data As a result, we choose to cluster genes based...

Ngày tải lên: 22/06/2014, 00:20

... down into spectrum In the gene expression analysis, we assume that any gene expression level is a comprehensive result of gene effects and condition effects, that is, the expression profile shift ... although the magnitude of expression may vary, we normalized each expression profile with its maximum, so all expression level is in the range between and As expected, the gene expression profile varies ... of the gene in each condition The fluctuation of the mean and standard deviation of expression levels of the rpoS, as shown in Figure 3, highlights the variation of expression level and expression...

Ngày tải lên: 22/06/2014, 19:20

... S: Onto-Tools: an ensemble of web-accessible, ontology -based tools for the functional design and interpretation of high- throughput gene expression experiments Nucleic Acids Res 2004, 32:W449-456 ... the lowest false discovery rate (FDR) Genes with a FDR of less than 10% were considered to present significant differential expression Thus, we studied gene expression profile of lymphocytes treated ... To explore genes modulated by radiation, we also compared gene expression profiles of lymphocytes treated with versus Gy T-test and ANOVA test [15,16] were used to compare the set of genes significantly...

Ngày tải lên: 09/08/2014, 09:22

... SpA gene expression signature and the presence of novel biomarkers of disease Gene expression microarray Unfractionated whole blood collection and RNA isolation were performed using the PAXgene ... Tables and based on likelihood calculations Pathway analysis of gene expression results Each gene was studied using a network analysis module within MetaCore™ bioinformatics software (GeneGo Inc, ... for each probe set: (1) a model in which gene expression is impacted by disease state alone; (2) a model in which gender is the sole influence on gene expression; (3) a model in which, after controlling...

Ngày tải lên: 09/08/2014, 14:22

... doi:10.1186/gb-2011-12-1-r8 Cite this article as: Herzog et al.: A novel informatics concept for highthroughput shotgun lipidomics based on the molecular fragmentation query language Genome Biology 2011 12:R8 Submit ... List of features: MS, lipid identification solely based on matching precursor masses observed in MS spectra; MS + MS/MS, lipid identification based on MS and MS/MS spectra - required for identifying ... to another lipid class, to mention only a few) and employ a palette of internal standards In high- throughput screens, intensities of precursor ions are directly output into the multivariate analysis...

Ngày tải lên: 09/08/2014, 22:23

... Candidate orf List No Candidate ISs Found ? Generation of Empty FinalReport Yes IS Prediction Web-basedInterface Generation of the annotation webpages ISsaga web -based annotationsystem New identified ... population, including high and low IS density, intercalated clusters of ISs and a wide variety of IS repeat_region repeat_region Gene CDS 19516 20316 /locus_tag="AM1_0019“ /db_xref="GeneID:5678856“ ... context (that is, flanking genes) for each annotated Page of IS, allowing identification of IS-induced gene disruption and rearrangements For example, the DRs flanking an IS are generated by insertion...

Ngày tải lên: 09/08/2014, 22:24

... to expressionplot@googlegroups.com Extracting biological meaning from high throughput data ExpressionPlot offers the gene expression community an easy-to-use tool for automated analysis of gene ... 2009, 4:14 22 ExpressionPlot [http://expressionplot.com/] 23 ExpressionPlot User’s Guide [http://expressionplot.com/wiki] 24 ExpressionPlot Google Group [http://groups.google.com/group/ expressionplot] ... particular genes or events The genelev tool generates barplots of gene levels (RPKM) with error bars (Figure 6a) The ecdf tool allows the user to visualize the levels or fold changes of a set of genes...

Ngày tải lên: 09/08/2014, 23:20

... library technology Keywords RNAi, next generation sequencing, barcode screening Background RNAi facilitates the assessment of gene function by silencing gene expression using synthetic anti-sense ... typically used in multiwell plate -based screening, shRNAs are commonly used for pooled competitive screening approaches, often called barcode screening Barcode screening offers improvements in ... any medium, provided the original work is properly cited High- throughput RNA interference screening using pooled shRNA libraries and next generation sequencing David Sims1, Ana M Mendes-Pereira1,...

Ngày tải lên: 09/08/2014, 23:20

... their expression or structure to selective degeneration of SNpc neurons, expression of genes within this neuronal population seems to be a suitable criterion for narrowing down the number of genes ... for PARK1-13 Of 199 genes, the cytogenetic locations of 20 overlapped with that of PARK loci, which were labeled PD candidate genes One of these genes, UCHL1, is a known PD gene, and were within ... multi-factorial disease-related genes requires methods based on priori knowledge about the candidates To prioritize the genes, several context -based approaches, ranging from phylogenetic profiling to biochemical...

Ngày tải lên: 10/08/2014, 05:21