Mining concepts from large SAGE gene expression matrices

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Mining concepts from large SAGE gene expression matrices (2003)

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by François Rioult , Céline Robardet , Sylvain Blachon , Bruno Crémilleux , Olivier G , Jean-françois Boulicaut

Venue:	In: Proceedings KDID’03 co-located with ECML-PKDD 2003, Catvat-Dubrovnik (Croatia
Citations:	13 - 8 self

BibTeX

@INPROCEEDINGS{Rioult03miningconcepts,
    author = {François Rioult and Céline Robardet and Sylvain Blachon and Bruno Crémilleux and Olivier G and Jean-françois Boulicaut},
    title = {Mining concepts from large SAGE gene expression matrices},
    booktitle = {In: Proceedings KDID’03 co-located with ECML-PKDD 2003, Catvat-Dubrovnik (Croatia},
    year = {2003},
    pages = {107--118}
}

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Abstract

Abstract. One of the crucial needs in post-genomic research is to analyze expression matrices (e.g., SAGE and microarray data) to identify a priori interesting sets of genes, e.g., sets of genes that are frequently co-regulated. Such matrices provide expression values for given biological situations (the lines) and given genes (columns). The inductive database framework enables to support knowledge discovery processes by means of sequences of queries that concerns both data processing and pattern querying (extraction, post-processing). We provide a simple formalization of a relevant pattern domain (language of patterns, evaluation functions and primitive constraints) that has been proved useful for specifying various analysis tasks. Recent algorithmic results w.r.t. the efficient evaluation (constraint-based mining) of the so-called inductive queries are emphasized and illustrated on a 90 × 12 636 human SAGE expression matrix. 1

Keyphrases

large sage gene expression matrix crucial need biological situation simple formalization various analysis task priori interesting set efficient evaluation expression matrix post-genomic research primitive constraint microarray data so-called inductive query expression value inductive database framework recent algorithmic result pattern querying data processing human sage expression matrix relevant pattern domain constraint-based mining knowledge discovery evaluation function

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