GenMiner: mining non-redundant association rules from integrated gene expression data and annotations.
GenMiner is an implementation of association rule discovery dedicated to the analysis of genomic data. It allows the analysis of datasets integrating multiple sources of biological data represented as both discrete values, such as gene annotations, and continuous values, such as gene expression measures. GenMiner implements the new NorDi (normal discretization) algorithm for normalizing and discretizing continuous values and takes advantage of the Close algorithm to efficiently generate minimal non-redundant association rules. Experiments show that execution time and memory usage of GenMiner are significantly smaller than those of the standard Apriori-based approach, as well as the number of extracted association rules.


BACKGROUND
The GenMiner software and supplementary materials are available at http://bioinfo.unice.fr/publications/genminer_article/ and http://keia.i3s.unice.fr/?Implementations:GenMiner


BACKGROUND
Supplementary data are available at Bioinformatics online.
Martinez
Ricardo
R
Laboratoire I3S, UNSA/CNRS UMR-6070, 2000 route des Lucioles, 06903 Valbonne, France.
Pasquier
Nicolas
N
Pasquier
Claude
C
D000465:Algorithms; D019295:Computational Biology; D015870:Gene Expression / Q000235:genetics*; D012984:Software