J Integr Bioinform - Profiling of genetic switches using boolean implications in expression data.

Tópicos

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Resumo

Correlation analysis assuming coexpression of the genes is a widely used method for gene expression analysis in molecular biology. Yet growing extent, quality and dimensionality of the molecular biological data permits emerging, more sophisticated approaches like Boolean implications. We present an approach which is a combination of the SOM (self organizing maps) machine learning method and Boolean implication analysis to identify relations between genes, metagenes and similarly behaving metagene groups (spots). Our method provides a way to assign Boolean states to genes/metagenes/spots and offers a functional view over significantly variant elements of gene expression data on these three different levels. While being able to cover relations between weakly correlated entities Boolean implication method also decomposes these relations into six implication classes. Our method allows one to validate or identify potential relationships between genes and functional modules of interest and to assess their switching behaviour. Furthermore the output of the method renders it possible to construct and study the network of genes. By providing logical implications as updating rules for the network it can also serve to aid modelling approaches.

Resumo Limpo

correl analysi assum coexpress gene wide use method gene express analysi molecular biolog yet grow extent qualiti dimension molecular biolog data permit emerg sophist approach like boolean implic present approach combin som self organ map machin learn method boolean implic analysi identifi relat gene metagen similar behav metagen group spot method provid way assign boolean state genesmetagenesspot offer function view signific variant element gene express data three differ level abl cover relat weak correl entiti boolean implic method also decompos relat six implic class method allow one valid identifi potenti relationship gene function modul interest assess switch behaviour furthermor output method render possibl construct studi network gene provid logic implic updat rule network can also serv aid model approach

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