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dc.contributor.authorSun, Peng
dc.contributor.authorGuo, Jiong
dc.contributor.authorEfficient, Jan Baumbach
dc.contributor.editorGiegerich, Robert
dc.contributor.editorHofestädt, Ralf
dc.contributor.editorNattkemper, Tim W.
dc.date.accessioned2017-07-26T14:12:12Z
dc.date.available2017-07-26T14:12:12Z
dc.date.issued2014
dc.identifier.isbn978-3-88579-629-9
dc.identifier.issn1617-5468
dc.description.abstractThe explosion of the biological data has dramatically reformed today's biological research. The need to integrate and analyze high-dimensional biological data on a large scale is driving the development of novel bioinformatics approaches. Biclustering, also known as simultaneous clustering or co-clustering, has been successfully utilized to discover local patterns in gene expression data and similar biomedical data types. Here, we contribute a new approach: Bi-Force. It is based on the weighted bicluster editing model, to perform biclustering on arbitrary sets of biological entities, given any kind of similarity function. We first evaluated the power of Bi-Force to solve dedicated bicluster editing problems by comparing Bi-Force with two existing algorithms in the BiCluE software package. We then followed a biclustering evaluation protocol from a recent review paper from Eren et al. and compared Bi-Force against eight existing tools: FABIA, QUBIC, Cheng and Church, Plaid, Bimax, Spectral, xMOTIFS and ISA. To this end, a suite of synthetic data sets as well as nine large gene expression data sets from Gene Expression Omnibus were analyzed. All resulting biclusters were subsequently investigated by Gene Ontology enrichment analysis to evaluate their biological relevance. The distinct theoretical foundation of Bi-Force (bicluster editing) is more powerful than strict biclustering. We thus outperformed existing tools with Bi-Force at least when following the evaluation protocols from Eren et al.. Bi-Force is implemented in Java and integrated into the open source software package of BiCluE. The software as well as all used data sets are publicly available aten
dc.language.isoen
dc.publisherGesellschaft für Informatik e.V.
dc.relation.ispartofGerman conference on bioinformatics 2014
dc.relation.ispartofseriesLecture Notes in Informatics (LNI) - Proceedings, Volume P-235
dc.titleLarge-scale bicluster editingen
dc.typeText/Conference Paper
dc.pubPlaceBonn
mci.reference.pages54-60
mci.conference.locationBielefeld
mci.conference.date28. September - 1. October 2014


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