:: DESCRIPTION
ExpressConverter is a file transformation tool that reads microarray data files in a variety of file formats and generates TIGR MultiExperiment Viewer file (.mev) as output so that the microarray data can be uploaded to the database with MADAM and analyzed with MIDAS and MEV.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
A-MADMAN (Annotation-based MicroArray DataMeta ANalysis tool) is an open source web application and gene chip analysis automation framework for annotation-based meta-analysis of data from public repositories (NCBI GEO).
::DEVELOPER
COMPUTATIONAL GENOMICS LABORATORY, Department of Biology, University of Padova, Italy.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bisognin A, Coppe A, Ferrari F, Risso D, Romualdi C, Bicciato S, Bortoluzzi S.
A-MADMAN: Annotation-based microarray data meta-analysis tool.
BMC Bioinformatics. 2009 Jun 29;10:201
:: DESCRIPTION
ArrayPipe is a web-based or standalone tool for the processing and analysis of microarray data. It provides functions for data visualization, background correction, normalization, detections of differentially expressed genes, comparison and highlighting of gene lists, as well as web-based spreadsheets for data mining.
::DEVELOPER
Brinkman Laboratory, Simon Fraser University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hokamp K, Roche FM, Acab M, Rousseau ME, Kuo B, Goode D, Aeschliman D, Bryan J, Babiuk LA, Hancock RE, Brinkman FS.
ArrayPipe: a flexible processing pipeline for microarray data.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W457-9. PMID: 15215429
:: DESCRIPTION
EVE (External Variance Estimation) is an software to detect differentially expressed genes using microarray data.You can download an R-script that works for data from the Affymetrix ATH1 GeneChip® microarray.
::DEVELOPER
Gruissem laboratory at the Institute of Plant Sciences
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wille, A., Gruissem, W., Bühlmann, P., Hennig, L. (2007)
EVE – External Variance Estimation increases statistical power for detecting differentially expressed genes.
Plant J 52, 561-569
:: DESCRIPTION
maxd is a data warehouse and visualisation environment for genomic expression data.maxd is made up of two software components:
maxdLoad2, for data storage, annotation and export,
maxdView, for data visualisation and analysis.
::DEVELOPER
Microarray Bioinformatics Group at the University of Manchester
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
The software is released under the terms of the Perl Artistic Licence .
:: DESCRIPTION
Magnolia is a microarray data management and export system for researchers who use PFGRC microarrays. Since it has been an obligation to submit microarray experiment data to public repositories for publishing the experimental results, collecting and storing the data is an essential step in microarray study. Implemented with H2 DBMS as the backend storage, Magnolia provides PFGRC array users with a series of intelligent entry form to collect the information or parameters of experiment, bio-source, sample, probe, slide, scan, expression, and normalization, which is MIAME compliant.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
This application is released under the GPL v3 License: View License
Contact the PFGRC’s Magnolia Development Team by email: magnolia@jcvi.org
:: DESCRIPTION
GeneXplorer is a web application for interactive microarray data visualization and analysis in a web environment. GeneXplorer allows users to browse a microarray dataset in an intuitive fashion. It provides simple access to microarray data over the Internet and uses only HTML and JavaScript to display graphic and annotation information. It provides radar and zoom views of the data, allows display of the nearest neighbors to a gene expression vector based on their Pearson correlations and provides the ability to search gene annotation fields.
::DEVELOPER
Gavin Sherlock etc.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rees, C.A., Demeter, J., Matese, J.C., Botstein, D. and Sherlock, G. (2004).
GeneXplorer: an interactive web application for microarray data visualization and analysis.
BMC Bioinformatics 5:41.
:: DESCRIPTION
ENIGMA – Expression Network Inference and Global Module Analysis. It is a software tool to analyze the modular structure of perturbational gene expression data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module.
::DEVELOPER
VIB (Flanders Interuniversitary Institute for Biotechnology)
Bioinformatics and Evolutionary Genomics Research Group at Ghent University
:: SCREENSHOTS
Command Line Tool
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
If you use ENIGMA in your research, please cite:
Steven Maere, Patrick Van Dijck, Martin Kuiper (2008) Extracting expression modules from perturbational gene expression compendia. BMC Systems Biology 2:33 (PubMed, BMC)
:: DESCRIPTION
NIA Array Analysis Tool is designed to test statistical significance of gene microarray data, visualize the results, and provide links to clone information and gene index.
Arrayjoin Tool is designed for compiling an input file from multiple scanner files.
ANOVA Tool – Statistical analysis is based on the single-factor ANalysis Of VAriance
Hierarchical clustering of tissues is done using the average distance method.
Principal component analysis (PCA) is done using the Singular Value Decomposition (SVD) method that generates eigenvectors both for rows and columns of the log-transformed data matrix (Gabriel 1971.
Pattern matching can be used to find genes with expression pattern similar to some other gene (or group of genes).
Gene list analysis – Getting information on selected genes is one of most important components of microarray analysis.
::DEVELOPER
Laboratory of Genetics, National Institute on Aging, NIH
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Reference:
Sharov, A.A., Dudekula, D.B., Ko, M.S.H. 2005. A web-based tool for principal component and significance analysis of microarray data. Bioinformatics, 21(10): 2548-9. Epub 2005 Feb 25. PMID: 15734774
