@misc{10481/51463,
year = {2018},
month = {4},
url = {http://hdl.handle.net/10481/51463},
abstract = {Applying differentially expressed genes (DEGs) to identify feasible biomarkers in diseases
can be a hard task when working with heterogeneous datasets. Expression data are
strongly influenced by technology, sample preparation processes, and/or labeling methods.
The proliferation of different microarray platforms for measuring gene expression increases
the need to develop models able to compare their results, especially when different technologies
can lead to signal values that vary greatly. Integrative meta-analysis can significantly
improve the reliability and robustness of DEG detection. The objective of this work was to
develop an integrative approach for identifying potential cancer biomarkers by integrating
gene expression data from two different platforms. Pancreatic ductal adenocarcinoma
(PDAC), where there is an urgent need to find new biomarkers due its late diagnosis, is an
ideal candidate for testing this technology. Expression data from two different datasets,
namely Affymetrix and Illumina (18 and 36 PDAC patients, respectively), as well as from 18
healthy controls, was used for this study. A meta-analysis based on an empirical Bayesian
methodology (ComBat) was then proposed to integrate these datasets. DEGs were finally
identified from the integrated data by using the statistical programming language R. After
our integrative meta-analysis, 5 genes were commonly identified within the individual analyses
of the independent datasets. Also, 28 novel genes that were not reported by the individual
analyses (`gained' genes) were also discovered. Several of these gained genes have
been already related to other gastroenterological tumors. The proposed integrative metaanalysis has revealed novel DEGs that may play an important role in PDAC and could be
potential biomarkers for diagnosing the disease.},
organization = {This work was supported by the
Instituto de Salud Carlos III (grant number
DTS15/00201 to OC), Ministerio de Economía Competitividad (the Spanish Ministry of
Economy and Competitiveness) (grant number
TIN2015-71873-R to IR), Consejería de Salud,
Junta de Andalucía (PIN-0474-2016 to JP),
Consejería de Economía, Innovación, Ciencia y
Empleo, Junta de Andalucía (P12-TIC-2082 to
IR) and the University de Granada (grant
number 15/13 to OC). The funders had no role
in study design, data collection and analysis,
decision to publish, or preparation of the
manuscript.},
publisher = {Public Library of Science (PLOS)},
title = {Integrative multi-platform meta-analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers},
doi = {10.1371/journal.pone.0194844},
author = {Irigoyen Medina, Antonio and Jiménez Luna, Cristina and Benavides, Manuel and Caba Pérez, Octavio and Gallego, Javier and Ortuño, Francisco M. and Guillen-Ponce, Carmen and Rojas Ruiz, Ignacio and Aranda, Enrique and Torres, Carolina and Prados Salazar, José Carlos},
}