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| Bioinformatics methods and techniques for microarray gene expression data analysis, clustering, pattern discovery, statistics , machine learning and visualization. |
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The Microarray protocol from Brown's lab
protocol
Part of MGuid Complete guide to Microarraying for the molecular biologist from the Brown Lab at Stanford University.
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Collection of papers on microarray data analysis
recommended
review
Resources maintained by Wentian Li.
This is a collection of papers (so far, ~1020 papers, excluding the unpublished preprints) with emphasis on analysis of microarray (a.k.a. DNA chip) data. (Papers on microarray technology itself are not usually in.) ...
Literature on Microarray Data Analysis
new recommended
review
Literature on microarray overview, experimental design, normalization, identification of differentially expressed genes, classification, cluster analysis and other unsupervised methods. (Anja von Heydebreck, Merck) ...
Bibliography on microarray data analysis
new recommended
review
This is a collection of papers (so far, ~1310 papers, excluding the unpublished preprints) with emphasis on analysis of microarray (a.k.a. DNA chip) expression data. (Papers on microarray technology itself are not usually in. Also, these topics are not really ...
RMA expression measure of Affy chips (Introduction and Papers)
review
Some papers discussing the RMA methodology. From Speedy Berkeley group.
The RMA (Robust Multichip Average) expression measure is for Affymetrix Genechip arrays. It fits a robust linear model at the probe level. ...
Microarray Software Comparison
new
review
Comparision of software used in microarray analysis (by Leung Yuk Fai, Harvard University)
Software includes:
Probe/primer design software
Image analysis software
Data preprocessing software
Data mining software
Turnkey/Enterprise system
Compr ...
Microarray Data Analysis (statweb)
top rated
site
Microarrays are a new technology to investigate the expression levels of thousands of genes simultaneously. Microarrays present new statistical problems because the data is very high dimensional with very little replication. Methods of adjustment for multiple ...
The MicroArray Explorer
new
database
Microarray Explorer (MAExplorer) is a Java-based data-mining facility for cDNA or oligonucleiotide microarray databases. It may be downloaded and run as a stand-alone application on your computer. Its exploratory data analysis environment provides tools for th ...
Pather classification system gene expression data analysis
software
Pather online tools can be used for microarray data intrepretation. Multiple gene lists can be mapped to PANTHER molecular function and biological process categories, as well as to biological pathways. The pathway visualization tool will display your exper ...
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Last update:  09-May-2008 07:16 pm
Related new papers and reviews
Ontology-based, Tissue MicroArray oriented, image centered tissue bank. BMC Bioinformatics. 2008;9 Suppl 4:S4
Authors: Viti F, Merelli I, Caprera A, Lazzari B, Stella A, Milanesi L
BACKGROUND: Tissue MicroArray technique is becoming increasingly important in pathology for the validation of experimental data from transcriptomic analysis. This approach produces many images which need to be properly managed, if possible with an infrastructure able to support tissue sharing between institutes. Moreover, the available frameworks oriented to Tissue MicroArray provide good storage for clinical patient, sample treatment and block construction information, but their utility is limited by the lack of data integration with biomolecular information. RESULTS: In this work we propose a Tissue MicroArray web oriented system to support researchers in managing bio-samples and, through the use of ontologies, enables tissue sharing aimed at the design of Tissue MicroArray experiments and results evaluation. Indeed, our system provides ontological description both for pre-analysis tissue images and for post-process analysis image results, which is crucial for information exchange. Moreover, working on well-defined terms it is then possible to query web resources for literature articles to integrate both pathology and bioinformatics data. CONCLUSIONS: Using this system, users associate an ontology-based description to each image uploaded into the database and also integrate results with the ontological description of biosequences identified in every tissue. Moreover, it is possible to integrate the ontological description provided by the user with a full compliant gene ontology definition, enabling statistical studies about correlation between the analyzed pathology and the most commonly related biological processes.
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