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Title: | Multiple platform assessmant of the EGF dependent transcritpome by microarrays and deep TAG sequencing analysis |
Author: | Llorens Torres, Franc Hummel, Manuela Pastor Durán, Xavier Ferrer, Anna Pluvinet Ortega, Raquel Vivancos, Ana Castillo, Ester Iraola Guzmán, Susana Mosquera, Ana M. González Barca, Eva Lozano Salvatella, Juan José Ingham, Matthew Dohm, Juliane C. Noguera, Marc Kofler, Robert Río Fernández, José Antonio del Bayés Colomer, Mònica Himmelbauer, Heinz Sumoy, Lauro |
Keywords: | Factor de creixement epidèrmic Genètica humana Microxips d'ADN Epidermal growth factor Human genetics DNA microarrays |
Issue Date: | 2011 |
Publisher: | BioMed Central |
Abstract: | 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. |
Note: | Reproducció del document publicat a: http://www.biomedcentral.com/1471-2164/12/326 |
It is part of: | Bmc Genomics, 2011, vol. 12, p. 326-330 |
URI: | http://hdl.handle.net/2445/36432 |
ISSN: | 1471-2164 |
Appears in Collections: | Articles publicats en revistes (Biologia Cel·lular, Fisiologia i Immunologia) |
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