Data analysis tools

Provided by Affymetrix. You can search and download the gene sequence and annotation of probe sets from this web site. Before using this tool, please register first at the Affymetrix web site.

Open source and open development software project for the analysis and comprehension of genomic data. It is based on R language and environment for statistical computing and graphics and provides many normalization algorithms for probe levels.

dChip using Li-Wong algorithm to produce data, it is different from the One-Step Tukey's Biweigh Estimate used by Affymetrix.

RMAExpress is a standlized GUI program for Windows to compute gene expression summary values for Affymetrix GeneChip data using the Robust Multichip Average expression summary. Please note that, this algorithm does not use MM probe cell information.

- MIDAS: Microarray Data Analysis System, a Java application, provides users with an intuitive interface to design analysis protocols combining one or more normalization and filtering steps.

- MEV: MultiExperiment Viewer, a versatile microarray data analysis tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery.

Implemented by TAIR, it includes:

- SeqViewer:  TAIR's new graphic display tool for Arabidopsis sequence and annotation.

- MapViewer: TAIR's comprehensive map visualization and alignment tool for sequence, genetic and physical maps is available.

- AraCyc Pathways: Arabidopsis biochemical pathways visualization and querying tool.

- Chromsome Map Tool: Draw maps of your favorite gene family.

Gene Expression Omnibus, gene expression/molecular abundance repository, and a curate, online resource for gene expression data browsing, query and retrieval.

Located at EBI. This is a public repository for microarray data. Provides microarray database containing many species.

Arabidopsis thaliana

NASCArrays is the Nottingham Arabidopsis Stock Centre's microarray database. Currently most of the data is for Arabidopsis thaliana experiments run by the NASC Affymetrix Facility. It includes two tools for searching:

- Spot History : allows you to see the pattern of gene expression over all slides in the database.

- Gene Swinger : If you have an interesting gene, this tool will show you for which experiment the gene expression varied most.

TAIR Microarray Expression Search allows searching for Arabidopsis thaliana Affymetrix microarray gene expression profiles.

National Institute of Agarobiological Science, processes rice genomic sequencing and provides some tools for rice research:

- Rice Expression Database (RED): RED holds raw and normalized data from expression profiles obtained by the Rice Microarray Project and other research groups.

- INtegrated rice genome Explorer (INE): a database integrating the genetic map, physical map and sequencing information of the rice genome.

Mouse

Mouse Genome Informatics provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.

A Database of the Drosophila Genome and provide tools for searching.

Other microarray cores in Taiwan

IPMB DNA Microarray Lab

IMB DNA microarray laboratory

DNA Microarray laboratory at Institute Molecular Biology, Academia Sinica.

High Throughput Genome Analysis Core Facility and Microarray & Gene Expression Analysis Core Facility (merged in May, 2008)

National Microarray & Gene Expression Analysis Core Facility of the National Research Program for Genomic Medicine at Yang-Ming University.