Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis
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 o...
| Autores: | , , , , , , , , , , , , , , , , , , |
|---|---|
| Tipo de documento: | artigo |
| Estado: | Versão publicada |
| Data de publicação: | 2011 |
| País: | España |
| Recursos: | Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
| Repositório: | Recercat. Dipósit de la Recerca de Catalunya |
| OAI Identifier: | oai:recercat.cat:10230/23285 |
| Acesso em linha: | http://hdl.handle.net/10230/23285 http://dx.doi.org/10.1186/1471-2164-12-326 |
| Access Level: | Acceso aberto |
| Palavra-chave: | Metabolisme Seqüència de nucleòtids Cultius cel·lulars |
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Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysisLlorens, FrancHummel, ManuelaPastor Ruiz, JavierFerrer Salvador, AnnaPluvinet, RaquelVivancos Prellezo, AnaCastillo Andreo, EstherIraola Guzmán, SusanaMosquera Miguel, AnaGonzález-Roca, EvaLozano, Juan JoséIngham, MatthewDohm, Juliane C.Noguera, MarcKofler, RobertRío, Jose Antonio delBayés, MònicaHimmelbauer, HeinzSumoy Van Dyck, LauroMetabolismeSeqüència de nucleòtidsCultius cel·lularsBackground: 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.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.RBioMed Central201520152011info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/23285http://dx.doi.org/10.1186/1471-2164-12-326reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésBMC Genomics. 2011; 12: 326info:eu-repo/grantAgreement/ES/2PN/SAF2004-06976© 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.http://creativecommons.org/licenses/by/2.0info:eu-repo/semantics/openAccessoai:recercat.cat:10230/232852026-05-29T05:05:01Z |
| dc.title.none.fl_str_mv |
Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis |
| title |
Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis |
| spellingShingle |
Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis Llorens, Franc Metabolisme Seqüència de nucleòtids Cultius cel·lulars |
| title_short |
Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis |
| title_full |
Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis |
| title_fullStr |
Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis |
| title_full_unstemmed |
Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis |
| title_sort |
Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis |
| dc.creator.none.fl_str_mv |
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 |
| author |
Llorens, Franc |
| author_facet |
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 |
| author_role |
author |
| author2 |
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 |
| author2_role |
author author author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Metabolisme Seqüència de nucleòtids Cultius cel·lulars |
| topic |
Metabolisme Seqüència de nucleòtids Cultius cel·lulars |
| description |
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. |
| publishDate |
2011 |
| dc.date.none.fl_str_mv |
2011 2015 2015 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
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article |
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publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10230/23285 http://dx.doi.org/10.1186/1471-2164-12-326 |
| url |
http://hdl.handle.net/10230/23285 http://dx.doi.org/10.1186/1471-2164-12-326 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
BMC Genomics. 2011; 12: 326 info:eu-repo/grantAgreement/ES/2PN/SAF2004-06976 |
| dc.rights.none.fl_str_mv |
http://creativecommons.org/licenses/by/2.0 info:eu-repo/semantics/openAccess |
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http://creativecommons.org/licenses/by/2.0 |
| eu_rights_str_mv |
openAccess |
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application/pdf application/pdf |
| dc.publisher.none.fl_str_mv |
BioMed Central |
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BioMed Central |
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reponame:Recercat. Dipósit de la Recerca de Catalunya instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
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Recercat. Dipósit de la Recerca de Catalunya |
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Recercat. Dipósit de la Recerca de Catalunya |
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