oligonucleotide array technologies for gene expression profiling

... 41 genes ↑ 56 genes ↑ gene ↓ DNA-repair gene ↓ genes ↑ gene ↓ 14 genes ↑ oncogenes/tumor related genes gene ↑ 11 genes ↓ genes ↑ 11 genes ↓ 13 genes ↑ 10 genes ↓ cell adhesion genes ↑ genes ↓ genes ... system genes ↑ 13 genes ↓ genes ↑ 19 genes ↓ genes ↑ 25 genes ↓ 13 genes ↓ genes ↑ genes ↓ 18 genes ↑ 10 genes ↓ signal transduction transcription gene ↑ genes ↓ 10 genes ↑ genes ↓ 22 genes ↑ genes ... transport genes ↑ 12 genes ↓ 11 genes ↑ 15 genes ↓ genes ↑ 15 genes ↓ development gene ↑ genes ↓ genes ↑ genes ↓ 12 genes ↑ genes ↓ calcium-binding genes ↑ genes ↓ gene ↓ apoptosis unknown genes ↓ genes...

Ngày tải lên: 18/06/2014, 15:20

... human GeneChips (U34A, U74A, U95A and U133A) for our multi-species cross-platform geneexpression analysis We first calculated gene- expression changes for each tested species and linked expression ... U133) GeneHopper [18,19], which uses the UniGene and HomoloGene databases to provide comparisons between arrays, is useful for linkage of selected genes of interest from different array platforms, ... from Affymetrix GeneChip arrays designed for different species [17,18], there are limited resources for simultaneous array- data analysis across multiple speciesspecific platforms (GeneChip IDs U34,...

Ngày tải lên: 09/08/2014, 20:20

... and Affymetrix microarrays In order to make the mapping file useful for studies involving grape microarray experiments, information from two microarray platforms was used, the Array Ready Oligo ... genes were predicted An accurate gene prediction and gene annotation is however still lacking for the whole sequence Using strict rules for homology definition, around half of the predicted genes ... expertise for standard two-color microarray normalization methods BMC Bioinformatics 2006, 7:467 Smyth GK: Linear models and empirical Bayes methods for assessing differential expression in microarray...

Ngày tải lên: 12/08/2014, 03:21

... normalization using ArrayGauge (Fujifilm) DNA microarray array data were deposited into the Center for Information Biology Gene Expression Database (CIBEX; accession: CBX 100) Quantification of genes using ... probes were spotted onto a GeneSlide platform (Toyo Kohan Co., Ltd Tokyo) using a Genex Arrayer Type-M (Kaken Geneqs, Inc., Chiba, Japan) GeneSlides were prehybridized at 80°C for hour, washed in 2× ... highlighted discrepancies in gene expression analyzed with different microarray technologies [5] Although a considerable number of studies have used DNA microarrays to genetically identify lung...

Ngày tải lên: 15/02/2014, 04:20

... anti-HER-2 therapy, alone or in combination Gene Expression Profiling Gene expression profiling (see Glossary, Appendix B) is an emerging technology for identifying genes whose activity may be helpful ... variability in gene expression For this reason, special care must be taken when tumors are sampled for gene expression analysis In general, macro- or micro-dissection of the samples is performed to ... model for microarray hybridizations Panel A: two-color scheme design Panel B: singlecolor design Sources of Variability in Gene Expression Analysis Gene expression analysis poses several general...

Ngày tải lên: 06/03/2014, 01:20

... the NT for each gene, the ratio is unchanged in Fig 2A,C for either reference gene or target gene, and using the ratio of NT/CT for target gene relative to NT/CT for reference gene controls for ... data for many genes simultaneously An internal standard CT is prepared for each gene, cloned to generate enough for >109 assays and CTs for up to 1000 genes are mixed together Each target gene ... standard CT for each gene in a SMIS Internal standard CT for each gene in an SMIS Multiplex Amplify with Reference Gene (e.g β-actin) Real-time measurement External standard curve for each gene measured...

Ngày tải lên: 10/04/2014, 22:32

... Bioanalyzer and the Agilent RNA 6000 Nano kit (data not shown) Gene expression profiling Aliquots of each sample were profiled for gene expression with or without globin mitigation using an automated ... Therefore, correlation between the amount of globin and gene expression signal is a robust metric for measuring globin interference Analysis of the distribution of microarray intensities for each ... of these used similar methodologies for objectively measuring expression profiling performance [14,22] Others have noted the benefits of usincDNA targets for profiling, although in some cases it...

Ngày tải lên: 18/06/2014, 16:20

... photolithography array technology as well as the general tools for bioinformatic analysis of these arrays Rapid advances in this field have brought new technologies to the market These include PCR arrays ... Motorola CodeLink microarray performance for gene expression profiling applications Nucleic Acids Res 2002, 30:e30 33 Oliphant A, Barker DL, Stuelpnagel JR, Chee MS: BeadArray technology: enabling ... of the genes that we discover in our experiments, strategies for systematic investigation are essential Gene expression profiling will essentially depend on valid statistical methods for estimating...

Ngày tải lên: 09/08/2014, 01:23

... that is, for three replicates, the gene should be detectable on at least two chips; for five replicates, the gene should be present on at least three DNA chips) Fold changes for gene expression ... false-positive genes To characterize gene expression patterns, hierarchical gene clustering was performed with a DNA-Chip Analyzer program [45,46] The algorithm was based on the distance between two genes ... Adarichev et al Table Array- based expression values of upregulated or downregulated genes in pre-inflamed joint Affy ID Description Gene Mean AN expression AN presence call Mean PA expression PA presence...

Ngày tải lên: 09/08/2014, 06:22

... median centred Genes for which expression values were present in less than 80% of samples were excluded Significance Analysis of Microarrays (SAM) [17] was performed to identify genes differentially ... did not confirm enrichment of relevant gene ontology categories For example, for up-regulated genes, the EASE score for extracellular matrix was 3.6E02 and for response to oxidative stress was ... of microarrays; Acknowledgements We thank Yvonne Hey and Stuart Pepper at the Cancer Research UK Affymetrix Genechip Microarray Service, Paterson Institute for Cancer Research, for performing...

Ngày tải lên: 09/08/2014, 09:20

... expression values for each gene based on cycle threshold (CT) values for each of the genes and the housekeeping gene GAPDH were generated Mean ± standard deviation (SD) values were generated from ... 19K-oligo human microarray slides to compare the gene expression profiles of OA, control and OP bone samples, with the aim being to identify altered gene expression in OA bone Microarray analysis was ... differential expression) are shown alongside the microarray results in Table In total, the differential expression levels of 20 genes were examined using real-time PCR Results for 16 genes reached...

Ngày tải lên: 09/08/2014, 10:21

... were performed using Genespringđ software (Agilent Technologies, Inc.) For each slide, scaled data were normalized to the 50th percentile value for each chip and to the median value for each gene ... therefore, it is not surprising that genes produced by these cells are overexpressed in tissues enriched for them This kind of bias is very common in gene expression studies performed in heterogeneous ... 35-minute incubation at 95C GeneChipđ Human Genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes) (Affymetrix UK Ltd.)...

Ngày tải lên: 09/08/2014, 14:20

... 2) These genes clearly separated early and LS RA Among these 719 genes, clusters (1 and 2) were distinct by their opposite gene- expression regulations for each stage In cluster 1, 503 genes were ... is a heterogeneous disease with distinct molecular forms, but to date, few studies have focused on different RA stages [17] Herein, we showed, for the first time, that gene- expression profiling ... agerelated gene expression profiles identifies common signatures of aging Bioinformatics 2009, 25:875-881 Olsen N, Sokka T, Seehorn CL, Kraft B, Maas K, Moore J, Aune TM: A gene expression signature for...

Ngày tải lên: 09/08/2014, 14:22

... of proteins in a microarray format and has several advantages over affinity capture of intact proteins These include, the homogeneity of digested proteins (typically in the form of tryptic peptides), ... used to assay the same protein target (similarly to Affymetrix DNA oligonucleotide arrays, where up to 20 oligonucleotides may be generated against the same mRNA sequence http://www.affymetrix.com), ... approach allows for a more straightforward and faster route, suitable for peptides of 10 amino acids and longer, while the slower enrichment approach provides a better alternative for shorter peptides...

Ngày tải lên: 11/08/2014, 00:22

... related genes were identified ranging from general defence-related genes (metallothioneins, thaumatin and universal stress genes) to more specific oomycete defence-related genes (pathogenesis ... Quantitative gene expression analysis Expression analyses of nine genes were conducted at 0, 3, 6, 12, 24 and 48 hours post infection (hpi) to validate if the pyrosequencing data reflected their gene expression ... available through accession numbers TSA JO840460-JO840468 Quantitative gene expression analysis Nine genes were selected for gene expression analysis and included: Thaumatin, thaumatin-like, metallothionein-...

Ngày tải lên: 11/08/2014, 11:21

... was Stage 1: 50°C for 30 min; Stage 2: 95°C for 15 min; Stage 3: 94°C for 15 sec, 55°C for 30 sec; and 72°C for 30 sec, repeated for 30 cycles Melting curve analysis was performed to verify product ... are averaged gene expression changes for different replicates Comparative analysis of host gene expression responses between HPAI-H5N1 and RG modified H5N1 virus infections Gene expression data ... of gene expression at different time-points (Figure 1) A total of 189 genes were found common between all the time points Expression pattern of most of the apoptotic genes was similar and formed...

Ngày tải lên: 12/08/2014, 01:21

... validation of gene array results We validated the results obtained with the gene array by Real Time RT-PCR using the same endothelial total RNA extract that was used for the gene array analysis ... The different gene expression patterns were analyzed using Array Assist version 5.0 (Stratagene, La Jolla, CA, USA), which calculates background-adjusted, normalized, and log-transformed intensity ... mRNA [37] Relative expression levels were calculated for each sample after normalization against the housekeeping gene GAPDH, using the ΔΔCt method for comparing relative fold expression differences...

Ngày tải lên: 12/08/2014, 14:22

... cancers using gene expression profiling and artificial neural networks Nat Med 2001, 7:673-679 Dettling M, Bühlmann P: Boosting for tumor classification with gene expression data Bioinformatics 2003, ... informative genes from thousands of available genes The informative genes are those that have high discriminative powers, and have low correlations between each pair of them [16] Selecting informative ... For the data that contains negative values, we not perform log-transformation In microarray data, the gene dimension is extremely large compared to the small number of samples Many of these genes...

Ngày tải lên: 12/08/2014, 17:20

... still limited to a small number of genes Oligonucleotide array technology allows the simultaneous assessment of thousands of genes providing a global gene expression profiling of the response to a ... Independent verification of microarray results by measurement of gene expression with real time-PCR Independent verification of microarray results by measurement of gene expression with real time-PCR ... TGFβ-responsive transcripts included genes with roles in gene expression, matrix formation, cytoskeletal remodelling, signalling, cell proliferation, protein expression and degradation, cell adhesion...

Ngày tải lên: 12/08/2014, 18:21

... files), using the Affymetrix GeneChip® Operating Software Expression microarray data have been submitted to the National Center for Biotechnology Information's Gene Expression Omnibus repository ... of microarray experiments BMC Bioinformatics 2006, 7:49 Kennedy RE, Kerns RT, Kong X, Archer KJ, Miles MF: SScore: an R package for detecting differential gene expression without gene expression ... Affymetrix GeneChip® Mouse Genome 430 2.0 arrays containing 45,101 probe sets for over 39,000 transcripts, including 34,000 well characterized mouse genes, and bioinformatics tools to characterize expression...

Ngày tải lên: 14/08/2014, 08:20