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1) J-Express:
J-Express is a java application for the analysis of microarray
gene expression. Includes hierarchical clustering,
self-organizing maps, principal component analysis, k-means,
profile searching, and integrated tools for visualisation.
J-Express has been developed in the bioinformatics
research group at the Dept.
of Informatics, UoB by Bjarte Dysvik and Inge
Jonassen, and is available free of charge to academic
labs.
2) Genesight:
The analysis and mining tool integrated
into Biodiscovery's analysis suite specifically designed for
microarray data.
3) Cluster
and Treeview: Excellent programs created by Michael
Eisen et. al visualizing microarray data
in various forms such as hierarchical clustering and self
organizing maps and freely distributed to academic labs. Eisen
et al. (1998) PNAS 95:14863
4) SAM
(Statistical Analysis of Microarrays) A helpful, freely
available excel macro
The program
is described in the following paper, PNAS
2001 98: 5116-5121, (Apr 24), Tusher, Tibshirani and Chu
(2001): as a method
of correlating gene expression data to a wide variety
of clinical parameters including treatment, diagnosis categories,
survival time and time trends. Program also facilitates estimation
of False Discovery Rate for multiple testing.
"Significance analysis of microarrays applied
to the ionizing radiation response" (ps file). (pdf
version).
We also recommend the following Websites:
1) KEGG (Kyoto
Encyclopedia of Genes and Genomes) This internet database
is in the GenomeNet consortium, and described as a
Japanese network of database and computational services
for genome research and related research areas in molecular
and cellular biology.
2) SOURCE
a free resource for academic researchers capable of rapidly
updating annotation of thousands of genes in seconds. This
internet database is helpful for updating annotation of clone
sets based on unigene, clone ID, and/or accession number.
3) CLEAVER
4) DRAGON
DATABASE
5) GENECARDS
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