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...

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Detalles Bibliográficos
Autores: 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
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2011
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/23285
Acceso en línea:http://hdl.handle.net/10230/23285
http://dx.doi.org/10.1186/1471-2164-12-326
Access Level:acceso abierto
Palabra clave:Metabolisme
Seqüència de nucleòtids
Cultius cel·lulars
Descripción
Sumario: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.

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