GenMiner: Non-Redundant Association Rules Mining from Genomic Data

Ricardo Martinez, Nicolas Pasquier and Claude Pasquier
Submitted to Bioinformatics

Supplementary materials

GenMiner program

The genminer program can be downloaded here.

Data pre-processing

Gene expression measures are those used by Eisen et al (Eisen et al., 1998). This dataset is discretized using the NorDi algorithm at a 95% confidence level.

Gene annotations were collected from the following sources:

Gene Ontology: terms were retrieved from http://archive.geneontology.org/latest-termdb/go_daily-termdb-data.gz (version of 27th August 2007) ; annotations were retrieved from http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.sgd.gz (version of 24th August 2007) ; GOSlim terms were retrieved from http://www.geneontology.org/GO_slims/goslim_yeast.obo.
Literature: associations between yeast genes and pubmed ids were retrieved from ftp://genome-ftp.stanford.edu/pub/yeast/data_download/literature_curation/gene_literature.tab (version of 8th August 2007)
Patways: information concerning the metabolic pathways in which each gene is involved was retrieved from ftp://ftp.genome.jp/pub/kegg/pathway/organisms/sce/sce_gene_map.tab (version of 9th August 2007)
Phenotype: annotations were retrieved from ftp://genome-ftp.stanford.edu/pub/yeast/data_download/literature_curation/phenotypes.tab (version of 9th August 2007)
transcriptional regulators: the information of transcriptional regulators that bind to promoter regions were extracted from http://jura.wi.mit.edu/young_public/regulatory_network/binding_by_gene.tsv using a p-value threshold of 0.0005

Available Data files

Files	Descriptions
Eisen dataset	Expression ratios of 2465 Yeast genes under 79 biological conditions.
Microarray Experiments	Description of the 79 experiments.
Cutoffs	Under-expressed and over-expressed cutoff thresholds computed by NorDi.
Discretized expression measures	Discretization of expression measures performed by Nordi.
Data mining context	Data matrix of 2465 lines (genes) and 737 columns (discretized expression levels and annotations). Each line contains expression profiles over the 79 biological conditions (values discretized by NorDi) and at most 658 gene annotations (24 GOSlim terms, 14 pathways, 25 transcriptional regulators, 14 phenotypes and 581 pubmed IDs).
Equivalence classes	Frequent closed itemsets and their generators extracted by Close with a minsupport of 0.005. Each class if represented by a line of the form [Generator] [Closed itemset] n where 'n' is the number of items in the class
Exact associations rules	All exact association rules displayed in the form [antecedent] => [consequent] supp=s conf=c where 's' and c are the support and the confidence of the rule respectively
Approximate associations rules	All approximate association rules, with a confidence greater or equals to 0.5, displayed in the form [antecedent] -> [consequent] supp=s conf=c where 's' and c are the support and the confidence of the rule respectively