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Publication details

Document type
Journal articles

Document subtype
Full paper

Title
Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators

Participants in the publication
Luka A. Clarke (Author)
BIOISI - Instituto de Biossistemas e Ciências Integrativas
Hugo M. Botelho (Author)
Lisete Sousa (Author)
Dep. Estatística e Investigação Operacional
CEAUL - Centro de Estatística e Aplicações
Andre O. Falcao (Author)
Dep. Informática
LASIGE - LASIGE
Margarida D. Amaral (Author)

Scope
International

Refereeing
Yes

Summary
A meta-analysis of 13 independent microarray data sets was performed and gene expression profiles from cystic fibrosis (CF), similar disorders (COPD: chronic obstructive pulmonary disease, IPF: idiopathic pulmonary fibrosis, asthma), environmental conditions (smoking, epithelial injury), related cellular processes (epithelial differentiation/regeneration), and non-respiratory "control" conditions (schizophrenia, dieting), were compared. Similarity among differentially expressed (DE) gene lists was assessed using a permutation test, and a clustergram was constructed, identifying common gene markers. Global gene expression values were standardized using a novel approach, revealing that similarities between independent data sets run deeper than shared DE genes. Correlation of gene expression values identified putative gene regulators of the CF transmembrane conductance regulator (CFTR) gene, of potential therapeutic significance. Our study provides a novel perspective on CF epithelial gene expression in the context of other lung disorders and conditions, and highlights the contribution of differentiation/EMT and injury to gene signatures of respiratory disease.

Date of Submisson/Request
2015-06-01
Date of Acceptance
2015-07-14
Date of Publication
2015-07-29

Institution
BioISI - Biosystems & Integrative Sciences Institute

Where published
BMC GENOMICS

Publication Identifiers
ISSN - 0888-7543

Publisher
Elsevier BV

Volume
106
Number
5

Starting page
268
Last page
277

Document Identifiers
URL - http://www.sciencedirect.com/science/article/pii/s0888754315300203
DOI - https://doi.org/10.1016/j.ygeno.2015.07.005

Rankings
SCOPUS Q2 (2015) - 1.312 - Genetics

Keywords
transcriptome differentiation respiratory disease Cystic fibrosis meta-analysis


Export

APA
Luka A. Clarke, Hugo M. Botelho, Lisete Sousa, Andre O. Falcao, Margarida D. Amaral, (2015). Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators. BMC GENOMICS, 106, 268-277. ISSN 0888-7543. eISSN . http://www.sciencedirect.com/science/article/pii/s0888754315300203

IEEE
Luka A. Clarke, Hugo M. Botelho, Lisete Sousa, Andre O. Falcao, Margarida D. Amaral, "Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators" in BMC GENOMICS, vol. 106, pp. 268-277, 2015. 10.1016/j.ygeno.2015.07.005

BIBTEX
@article{12134, author = {Luka A. Clarke and Hugo M. Botelho and Lisete Sousa and Andre O. Falcao and Margarida D. Amaral}, title = {Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators}, journal = {BMC GENOMICS}, year = 2015, pages = {268-277}, volume = 106 }