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Model-based analysis of oligonucleotide arrays, dChip software Cheng Li (Joint work with Wing Wong) Statistics and Genomics Lecture 4 Department of Biostatistics
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In the demonstration, we will reproduce analysis for the 8 arrays (m,n,o,p,q,r,s, ... (Background Adjust: Yes, Normalization: Quantile, Store residuals: [unclicked] ...
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Create POS and NEG groups as best we can. How to compare (depends on down ... SAFER provides same raw materials (fitted values and residuals) for QC as Li and ...
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Title: Wst pna analiza danych pochodz cych z mikromacierzy DNA Author: ZBiot Last modified by: Grzegorz Koczyk Created Date: 11/2/2004 12:35:53 PM
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... GeneChip Data Analysis. Chip concepts and array design. Improving intensity estimation from probe ... Concepts of Array Design. PM to maximize hybridization ...
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Summaries of Affymetrix GeneChip probe level data By Rafael A. Irizarry PH 296 Project, Fall 2003 Group:Kelly Moore, Amanda Shieh, Xin Zhao Microarrays: Many Probes ...
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Title: Analysis of Affymetrix Microarrays Author: Gareth Palidwor Last modified by: gpalidwor Created Date: 1/18/2005 5:20:25 PM Document presentation format
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The power of gene expression profiling to unravel behaviour Cathy Fernandes, Jose Paya-Cano, Frans Sluyter, Ursula D'Souza, Robert Plomin, Leonard C Schalkwyk
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Department of Genetics & Center for Genome Sciences. Washington ... Base Line Array (linear); Quantile Normalization;Contrast Normalization; etc. S Mean of S ...
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Human Genome Project (http://genome.ucsc.edu/downloads.html) Gene Ontology Consortium ... Human Genome Project Date built: 28jun2002. URL:http://www.genome.ucsc.edu ...
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NASC. Normalisation and Analysis of the Affymetrix Data. David J Craigon. NASC ... Analyse down to one number per gene. NASC. What do we want to find out? ...
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Genomewide Copy Number Analysis
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The principle: have two denatured DNA strands bond together, ... Syringe-solenoid ink-jet dispenser. Contact (using rigid pin tools, similar to filter array) ...
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Biostatistics Bioinformatics Core Personnel Elizabeth Garrett, PhD Biostatistician Giovanni Parmigiani, PhD Biostatistician Data analysis and System support staff
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Global Gene Expression Profiling in Whole Blood Samples from Individuals ... Exposure to particulates induces systemic inflammation in the lung that can be ...
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Title: Microarray Data Analysis Author: Kath Last modified by: Janet Murray Created Date: 10/14/2003 5:52:40 PM Document presentation format: On-screen Show
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An Array of FDA Efforts in Pharmacogenomics Weida Tong Director, Center for Toxicoinformatics, NCTR/FDA Weida.tong@fda.hhs.gov CAMDA 08, Boku University, Vienna ...
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1 RetNet Team VI : Laboratoire de Bioinformatique et G nomique Int grative, Department of Structural Biology, IGBMC, 1 rue Laurent Fries, F-67404 Illkirch Cedex, ...
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... first use of the program. GeneCluster Capabilities. Dataset Preprocessing ... GeneCluster selects predictor genes of clinical status using a training data set, ...
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Gene expression profiling identifies molecular subtypes of gliomas Ruty Shai, Tao Shi, Thomas J Kremen, Steve Horvath, Linda M Liau, Timothy F Cloughesy, Paul S ...
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Detection and Restoration of Hybridization Problems in ... Akita Pref. Univ. a monolith? praise and censure. for microarray technology. ????. Admired: ...
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Gene expression studies of cancer: gene transcription signatures
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... microarray, gene expression profile, DNA chips, hybridization, array ... Cow (Bos taurus) Rice. Cotton. 180 organisms have had their genomes sequenced ...
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Between-replicate CNV reproducibility. A CNV call was considered replicated if there was a reciprocal overlap of at least 80% between CNVs in a pair-wise comparison.
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Download any sample from workgroup and create new experiments. Genespring GX ... Genespring GX either using your own licence or NASC licence (5 concurrent ...
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Quantile normalization: fit to average quantiles ... Quantile Method (RMA) ... Quantile normalization is very strong: highly expressed genes won't be equal ...
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Use microarrays to find heart circadian genes and liver circadian genes ... Using hypergeometric test (the 2nd generation of GoSurfer ) Obs22. Obs21. Gene List 2 ...
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The purpose of clustering is to group genes that display similar expression patterns together. ... The pair-wise distance matrix is calculated for all patterns/genes ...
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Major genomic instability would follow including massive gene losses ... to increase the odd-ratio (gene load, single CNV, larger-sized CNV), but more or less the same ...
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To understand and use some of the tools for exploring and pre ... 'Crop Circles' 'Ring of Fire' Lab 2.1. 38. NUSE Plots. Normalized. Unscaled. Standard. Errors ...
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tool for DNA microarray and ... three major bioinformatics issues are ... An important concept in ArrayTrack Create a gene list through data filtering and statistical ...
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To understand the structures of existing biological databases, ... Orthology describes genes in different species that derive from a common ancestor. ...
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Experimenter/protocol issues (comparing chips processed by different labs) ... Not appropriate when comparing highly heterogeneous samples (different tissues) ...
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MOLECULAR NEUROENDOCRINOLOGY RESEARCH GROUP. BIOMEDICAL DISCOVERY USING MICROARRAYS ... MOLECULAR NEUROENDOCRINOLOGY RESEARCH GROUP. FUNCTIONAL GENOMICS. 30, ...
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In silico Gene Function Prediction Using Ontology-based Pattern Identification. Paper Review ... OPI : Ontology-based Pattern Identification is a data-mining ...
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Mining for Low Abundance Transcripts in Microarray Data. Yi ... might be aberrant in obese and/or diabetic subjects. Nadler et al. (2000) PNAS. 20 March 2002 ...
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For each gene that is a target for the array, we have a known DNA sequence. ... Quantile normalization makes the overall distribution of intensity values across ...
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MDMS-A Web Tool to Manage & Analyze Gene Expression Microarray Data. Sachin Mathur ... Analysis of Early Lung Development dataset using MDMS. MDMS Demo ...
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AT version 2 (2002): in-house microarray core facility ... ArrayTrack contains pathways for human (134), rat (116) and mouse (124) ...
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Human Genetics Journal Club. November 17, 2003. Overall Plan. Oligo Array (Affymetrix U95A) ... rate of expression change on human lineage is higher in brain ...
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From autopsy patients. 151 samples completed on 133A and 133B Affymetrix oligonucleotide arrays. Patient samples- replicates, multiple sampling, progression, and ...
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Analysis of Exon Arrays. Slides provided by Dr. Yi Xing ... Probes from 600 bps near 3' end. Probes from each putative exon. Probeset has 11 PM, 11 MM probes ...
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A 24 mm long wire in the 45 nm technology node. 14. An Example ... Far Inductive Crosstalk. Impact of ... New compact physical models for far inductive noise. ...
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Probe: A 25mer oligo complemetary to a sequence of interest, attached to a glace ... These packages include: DMT, Spotfire, Genespring, STATA, Gene Data ...
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Microarray and ChIP-seq Data Analysis Victor Jin Department of Biomedical Informatics Ohio State University * * * * * * * * * * Xbp1 universal stress repressor, tbp1 ...
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mRNA is reverse transcribed to DNA, and if a complementary sequence is on the on ... labeled with a dye that will fluoresce and generate a signal that is monotonic ...
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The conentration of labels in the cDNA is measured! ... gar. Gene 6. 0.86. 0.84. 0.42. 0.84. 0.44. groo. Gene 5. 0.41. 0.21. 0.11. 0.26. 0.60. bas. Gene 4 ...
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... to the 3', middle and 5'-end of the house keeping genes such as GAPDH and Actin. ... present calls should be 25% ('A' mouse, rat, human arrays) ...
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Following discussions with Caroline, Christine, Danielle, Eric, Hugh, Ilhem, ... Affymetrix scanners transform message into light. The Engima scanner has low noise: ...
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The incoming directory is emptied automatically every few weeks. ... holds all experiments being loaded and processes them in an ordered fashion ...
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2. Intensity-dependent normalization (Yang, Speed) (Lowess local ... Global normalization cannot remove intensity-dependent biases. 3. Quantile Normalization ...
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... wildtype ('normal') mice compared with 3 mice with Cd36 ... Mouse data. set A. 18. BGX. Data: ygcr = log gene expression gene g, replicate r, condition c ...
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... provide critical background information for malaria control strategies based on ... Senior System analyst, National Center for Biotechnology Information, National ...
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Use Cumulative Distribution Function (cdf) to determine the intensity of the ... DataMining Tool 3.0 (DMT 3.) -- Affymetrix. GeneSpring 5.0 -- Silicon Genetics ...
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For details on reading vignettes, see. the openVignette help page. openVignette() Please select (by number) a vignette. 1: affy primer. 2: affy: Built-in ...
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