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Of the previously mentioned tools, MADIBA is most similar to WebGestalt [ 12], which also obtains information from different data sources and provides an integrated set of analysis tools to assist researchers in mining this gene set.
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Thus, we mined the gene repertoire of B. rhizoxinica (Lackner, 2011b) for potential molecular infection mechanisms known from pathogenic bacteria.
We created the PDG-ACE algorithm to overcome this limitation by mining Entrez Gene text to identify biomedical keywords that are common and significantly over-represented in the descriptions of genes at a selected locus pair, relative to all locus pairs in the genome.
We then mined this data to identify candidate genes in pathways predicted to be involved in insecticide resistance.
We mined this network to detect composite genes using FusedTriplets (Jachiet et al. 2013), with a stringency E value of 10E-10.
Here, we mined the genes of 3,008 viral genomes and detected 8 15% composite sequences.
R.J.S. and K.M.D. mined the genes, analysed the expression patterns, performed extraction for IAA measurements and co-wrote the paper.
Methods for mining gene sequences for transcriptionally relevant information have become possible with the growing body of knowledge about mammalian genomes, gene expression and regulation of gene expression (See [5] for review).
Scheinin, I. et al. CanGEM: mining gene copy number changes in cancer.
"Molecular Interaction Search Tool MISTT): an integrated resource for mining gene and protein interaction data". Nucleic Acids Res, 46, D1, Pp.
Several tools are freely available for mining gene expression data repositories based on similarity with an input signature in a similar manner to cMap.
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