Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

Llorens, Franc; Hummel, Manuela; Pastor Ruiz, Javier; Ferrer Salvador, Anna; Pluvinet, Raquel; Vivancos Prellezo, Ana; Castillo Andreo, Esther; Iraola Guzmán, Susana; Mosquera Miguel, Ana; González-Roca, Eva; Lozano, Juan José; Ingham, Matthew; Dohm, Juliane C.; Noguera, Marc; Kofler, Robert; Río, Jose Antonio del; Bayés, Mònica; Himmelbauer, Heinz; Sumoy Van Dyck, Lauro

Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

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dc.contributor.author Llorens, Francca
dc.contributor.author Hummel, Manuelaca
dc.contributor.author Pastor Ruiz, Javierca
dc.contributor.author Ferrer Salvador, Annaca
dc.contributor.author Pluvinet, Raquelca
dc.contributor.author Vivancos Prellezo, Anaca
dc.contributor.author Castillo Andreo, Estherca
dc.contributor.author Iraola Guzmán, Susanaca
dc.contributor.author Mosquera Miguel, Anaca
dc.contributor.author González-Roca, Evaca
dc.contributor.author Lozano, Juan Joséca
dc.contributor.author Ingham, Matthewca
dc.contributor.author Dohm, Juliane C.ca
dc.contributor.author Noguera, Marcca
dc.contributor.author Kofler, Robertca
dc.contributor.author Río, Jose Antonio delca
dc.contributor.author Bayés, Mònicaca
dc.contributor.author Himmelbauer, Heinzca
dc.contributor.author Sumoy Van Dyck, Lauroca
dc.date.accessioned 2015-03-26T10:51:33Z
dc.date.available 2015-03-26T10:51:33Z
dc.date.issued 2011ca
dc.description.abstract Background: Epidermal Growth Factor (EGF) is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer. Results: By applying a procedure for cross-platform data meta-analysis based on RankProd and GlobalAncova tests, we establish a well validated gene set with transcript levels altered after EGF treatment. We use this robust gene list to build higher order networks of gene interaction by interconnecting associated networks, supporting and extending the important role of the EGF signaling pathway in cancer. In addition, we find an entirely new set of genes previously unrelated to the currently accepted EGF associated cellular functions. Conclusions: We propose that the use of global genomic cross-validation derived from high content technologies (microarrays or deep sequencing) can be used to generate more reliable datasets. This approach should help to improve the confidence of downstream in silico functional inference analyses based on high content data.en
dc.description.sponsorship This work was supported by start up funds from the institute for Predictive and Personalized Medicine of Cancer and the Center for Genomic Regulation [core funding to L.S.]; by the Spanish Ministry of Science and Technology [grant number SAF2004-06976 to L.S., Juan de la Cierva researcher contract to F.L., and technician contracts for support of technological infrastructures to E.G. and A.F.]; and by excellence in research team recognitions by the Catalan government, Departament de Innovació, Universitats i Ensenyament, Generalitat de Catalunya [Singular Research Group award number SGR2005-404 to L.S and SGR2009-0366 to J.A.D.R., by the Instituto de Salud Carlos III Fondo de Investigaciones Sanitarias [grant number PI10/01154 to L.S.] and to J.A.D.R, by the Spanish Ministry of Science and Technology to F.L. and J.A.D.Ren
dc.format.mimetype application/pdfca
dc.identifier.citation Llorens F, Hummel M, Pastor X, Ferrer A, Pluvinet R, Vivancos A, Castillo E, Iraola S, Mosquera AM, González E, Lozano J, Ingham M, Dohm JC, Noguera M, Kofler R, del Río J, Bayés M, Himmelbauer H, Sumoy L. Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis. BMC Genomics. 2011; 12: 326. DOI 10.1186/1471-2164-12-326ca
dc.identifier.doi http://dx.doi.org/10.1186/1471-2164-12-326
dc.identifier.issn 1471-2164ca
dc.identifier.uri http://hdl.handle.net/10230/23285
dc.language.iso engca
dc.publisher BioMed Centralca
dc.relation.ispartof BMC Genomics. 2011; 12: 326
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/SAF2004-06976
dc.rights © 2011 Llorens et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.ca
dc.rights.accessRights info:eu-repo/semantics/openAccessca
dc.rights.uri http://creativecommons.org/licenses/by/2.0
dc.subject.other Metabolismeca
dc.subject.other Seqüència de nucleòtidsca
dc.subject.other Cultius cel·lularsca
dc.title Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysisen
dc.type info:eu-repo/semantics/articleca
dc.type.version info:eu-repo/semantics/publishedVersionca

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