Analysis and Management of Microarray Gene Expression Data
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
Microarray experiments require careful planning and choice of analysis tools in order to get the most out of the data generated, especially considering the associated significant cost and effort. Microarray experiments also require careful documentation, often residing in local databases and/or submitted to public repositories. An often bewildering assortment of choices is available for experimental design, data preprocessing, data analysis (e.g., differential gene expression, classification), and data management. This unit covers the basic steps and common applications for planning, data processing, and data management of microarray experiments, and provides guidance to making choices based on the goals and practical realities of the experiment, as well as the authors' experience in this area.
Keywords: microarray; experimental design; data preprocessing; data analysis; databases; gene expression
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PDF or HTML at Wiley Online LibraryTable of Contents
- Experimental Design
- Data Preprocessing
- Expression and Differential Expression
- Classification
- Looking at Gene Sets
- Databases
- Conclusions
- Literature Cited
- Figures
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Figure 19.6.1 Steps involved in carrying out a complete microarray experiment. View Image -
Figure 19.6.2 (A ) Plot of M versus A for a two‐channel microarray assay (see text). The dashed horizontal line is the line M = m where m is the median of M over all reporters. The solid curve represents a global loess fit. (B ) Plot of M versus A for the data from panel A after normalization by the global constant m . The solid curve represents a global loess fit and illustrates that this normalization did not eliminate intensity‐dependent biases. (C ) Plot of M versus A for the data from panel A after global loess normalization. All global loess fitting and normalization performed with the Bioconductor marray R package. View Image -
Figure 19.6.3 (A ) Plot of M versus A for a two‐channel microarray assay. Each curve represents a lowess fit to one of the print‐tips. Data generated with the Bioconductor sma R package, using the MouseArray dataset provided therein. (B ) Plot of M versus A for the data from panel A after print‐tip lowess normalization (performed with the Bioconductor sma R package). View Image -
Figure 19.6.4 Result of hierarchical clustering of both genes and samples for twelve one‐channel assays, using centered Pearson correlation and the Eisen's TreeView software (http://rana.lbl.gov/EisenSoftware.htm). The sample tree is along the top and the gene tree is along the side. Brighter green represents higher signal intensity. View Image -
Figure 19.6.5 Simple example of a decision tree. View Image
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| Affymetrix statistical algorithms reference guide (MAS 5.0). | |
| http://www.affymetrix.com//support/downloads/manuals/data_analysis_fundamentals_manual.pdf | |
| Affymetrix Data Analysis Fundamentals Manual. | |
| http://www.ebi.ac.uk/arrayexpress/ | |
| The ArrayExpress repository | |
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| The AlignACE Web site. | |
| http://www1.amershambiosciences.com/aptrix/upp01077.nsf/Content/microarrays_analysis | |
| ArrayVision image analysis software. | |
| http://base.thep.lu.se/ | |
| The BASE ‐ BioArray Software Environment Web site. | |
| http://www.gene‐regulation.com/pub/databases.html | |
| The BIOBASE Web site, which includes TRANSFAC. | |
| http://www.bioconductor.org | |
| The Bioconductor project Web site. | |
| http://www.genomethods.org/caged | |
| The CAGED Web site. | |
| http://david.abcc.ncifcrf.gov | |
| DAVID Web site at NIAID, where EASE is also available. | |
| http://www.dchip.org | |
| dChip software, with links to references and tutorials. | |
| http://www.cbcb.umd.edu/software/ELPH | |
| The ELPH Gibbs Sampler Web site. | |
| http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene | |
| The Entrez Gene Web site. | |
| http://www.ncbi.nlm.nih.gov/Genbank | |
| The GenBank Web site. | |
| http://www.ncbi.nlm.nih.gov/geo/ | |
| The Gene Expression Omnibus (GEO) repository. | |
| http://www.geneontology.org/ | |
| The Gene Ontology Project Web site. | |
| http://www.moleculardevices.com/pages/software/gn_genepix_pro.html | |
| GenePix image analysis software. | |
| http://www.broad.mit.edu/gsea | |
| The Gene Set Enrichment Analysis (GSEA) Web site. | |
| http://www.genmapp.org/ | |
| The GenMAPP project Web site. | |
| http://www.gusdb.org/ | |
| The GUS (Genomics Unified Schema) Web site containing the RAD software. | |
| http://mordor.cgb.ki.se/cgi‐bin/jaspar2005/jaspar_db.pl | |
| The JASPAR Web site. | |
| http://www.genome.jp/kegg/pathway.html | |
| The KEGG Pathway database. | |
| http://meme.sdsc.edu | |
| The MEME Web site. | |
| http://www.mged.org | |
| The MGED Web site with links for MIAME, MAGE, and MGED Ontology. | |
| http://www.ebi.ac.uk/miamexpress/ | |
| The MIAMExpress annotation and submission tool. | |
| http://www.mysql.com/ | |
| The MySQL open source database Web site. | |
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| The PaGE Web site. | |
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| The PAM Web site. | |
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| The PostgreSQL open source database Web site. | |
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| RMAExpress Web site, which includes relevant references. | |
| http://www‐stat.stanford.edu/∼tibs/SAM/ | |
| The SAM Web site | |
| http://rana.lbl.gov/manuals/ScanAlyzeDoc.pdf | |
| ScanAlyze image analysis software. | |
| http://experimental.act.cmis.csiro.au/Spot/index.php | |
| Spot image analysis software. | |
| http://genome‐www5.stanford.edu/download/ | |
| The Stanford Microarray Database (SMD) software download site. | |
| http://genome‐www5.stanford.edu/resources/databases.shtml | |
| The Stanford Microarray Database (SMD). | |
| http://www.stratagene.com | |
| The Stratagene Web site. | |
| http://www.tm4.org/ | |
| TM4: a package of open source software for microarray analysis, comprising MADAM, SpotFinder, MIDAS, and MeV. | |
| http://www.stat.berkeley.edu/users/terry/zarray/TechReport/589.pdf | |
| Technical report on normalization for two‐channel arrays by Y.H. Yang, S. Dudoit, P. Luu, and T.P. Speed. | |
| http://159.149.109.16:8080/weederWeb/ | |
| The Weeder Web site. | |
| http://www.cs.waikato.ac.nz/ml/weka/ | |
| The WEKA web resource. |
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