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

Autor: Marc Noguera, José Antonio del Río, Anna Ferrer, Eva González, Ester Castillo, Juanjo Lozano, Ana Vivancos, Susana Iraola, Juliane C. Dohm, Heinz Himmelbauer, Franc Llorens, Raquel Pluvinet, Matthew Ingham, Lauro Sumoy, Robert Kofler, Xavier Pastor, Mònica Bayés, Manuela Hummel, Ana M Mosquera
Rok vydání: 2011
Předmět:
Zdroj: BMC Genomics
BMC Genomics, Vol 12, Iss 1, p 326 (2011)
ISSN: 1471-2164
Popis: 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. 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.R
Databáze: OpenAIRE
Externí odkaz: