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T. rubrum had been shortlisted for sequencing by the Fungal Genome Initiative (FGD white paper, 2004), yet expressed sequence tag (EST -based mRNA transcription profiling and microarray tEST -basedare used extensively to characterize gene functions and discover functionally related genes needed for developmRNAal and behavioural processes [ 11, 12].
It can be used to discover functionally related genes for a given gene, group of genes, or set of function terms.
Large-scale gene expression measured by microarrays is a valuable and under-exploited data resource to discover functionally coupled genes.
We have also performed correlation link confirmation among subsets and correlation conservation analysis to discover functionally related genes.
To further investigate WGCNA's ability to discover functionally important groups of genes, we turned to an independent data set from Zhou et al (2007) [ 8].
Therefore, genotyping a diverse germplasm set using high-throughput genotyping assays is of particular interest for rice breeders to discover functionally relevant genes and new alleles [ 22].
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For inferring functional linkages from DNA microarray evidence, we employ the divide-test-integrate approach [1] for discovering functionally informative cases of mRNA co-expression.
As an initial approach to discovering functionally significant polymorphisms of the PPARA promoters, we used the web-based program PromoLign (http://polly.wustl.edu/promolign/main.html) [23], to identify nucleotide variants within 10 kb of the transcription start site.
Biclustering algorithms for microarray data aim at discovering functionally related gene sets under different subsets of experimental conditions.
It is a flexible and powerful tool for rapidly discovering functionally similar gene products from fast-expanding GO annotation databases.
It has been used for detecting differentially expressed genes [ 1- 4], discovering disease markers [ 5], discovering functionally related genes, and clustering genome-wide expression patterns [ 6- 9].
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