Including transcription factor information in the superparamagnetic clustering of microarray data

dc.creatorMARIA DEL PILAR MONSIVAIS ALONSO
dc.creatorJORGE CARLOS NAVARRO MUÑOZ
dc.creatorLINA RAQUEL RIEGO RUIZ
dc.creatorROMAN LOPEZ SANDOVAL
dc.creatorHARET CODRATIAN ROSU
dc.date2010
dc.date.accessioned2018-11-19T13:50:49Z
dc.date.available2018-11-19T13:50:49Z
dc.identifierhttp://ipicyt.repositorioinstitucional.mx/jspui/handle/1010/919
dc.identifier.urihttp://repositorioslatinoamericanos.uchile.cl/handle/2250/2252049
dc.description"In this work, we modify the superparamagnetic clustering algorithm (SPC) by adding an extra weight to the interaction formula that considers which genes are regulated by the same transcription factor. With this modified algorithm that we call SPCTF, we analyze Spellman et al. microarray data for cell cycle genes in yeast, and find clusters with a higher number of elements compared with those obtained with the SPC algorithm. Some of the incorporated genes by using SPCFT were not detected at first by Spellman et al. but were later identified by other studies, whereas several genes still remain unclassified. The clusters composed by unidentified genes were analyzed with MUSA, the motif finding using an unsupervised approach algorithm, and this allow us to select the clusters whose elements contain cell cycle transcription factor binding sites as clusters worth of further experimental studies because they would probably lead to new cell cycle genes. Finally, our idea of introducing available infor-mation about transcription factors to optimize the gene classification could be implemented for other distance-based clustering algorithms."
dc.formatapplication/pdf
dc.languageeng
dc.publisherElsevier
dc.relationinfo:eu-repo/semantics/altIdentifier/DOI/https://doi.org/10.1016/j.physa.2010.09.006
dc.relationcitation:M.P. Monsiváis-Alonso, J.C. Navarro-Muñoz, L. Riego-Ruiz, R. López-Sandoval, H.C. Rosu, Including transcription factor information in the superparamagnetic clustering of microarray data, Physica A: Statistical Mechanics and its Applications, Volume 389, Issue 24, 2010, Pages 5689-5697, ISSN 0378-4371, http://dx.doi.org/10.1016/j.physa.2010.09.006.
dc.rightsinfo:eu-repo/semantics/openAccess
dc.rightshttp://creativecommons.org/licenses/by-nc-nd/4.0
dc.subjectinfo:eu-repo/classification/Autor/Superparamagnetic clustering
dc.subjectinfo:eu-repo/classification/Autor/Similarity measure
dc.subjectinfo:eu-repo/classification/Autor/Microarrays
dc.subjectinfo:eu-repo/classification/Autor/Cell cycle genes
dc.subjectinfo:eu-repo/classification/Autor/Transcription factors
dc.subjectinfo:eu-repo/classification/cti/1
dc.titleIncluding transcription factor information in the superparamagnetic clustering of microarray data
dc.typeArtículos de revistas
dc.typeinfo:eu-repo/semantics/acceptedVersion
dc.audiencegeneralPublic


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