Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA).

<h4>Background</h4>Our objective was to develop a consistent molecular definition of psoriasis. There have been several published microarray studies of psoriasis, and we compared disease-related genes identified across these different studies of psoriasis with our own in order to establi...

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Autores principales:	Mayte Suárez-Fariñas, Michelle A Lowes, Lisa C Zaba, James G Krueger
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9b137d3b41a24ffb9207d5d862ca68e7
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spelling	oai:doaj.org-article:9b137d3b41a24ffb9207d5d862ca68e72021-11-25T06:24:26ZEvaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA).1932-620310.1371/journal.pone.0010247https://doaj.org/article/9b137d3b41a24ffb9207d5d862ca68e72010-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20422035/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Our objective was to develop a consistent molecular definition of psoriasis. There have been several published microarray studies of psoriasis, and we compared disease-related genes identified across these different studies of psoriasis with our own in order to establish a consensus.<h4>Methodology/principal findings</h4>We present a psoriasis transcriptome from a group of 15 patients enrolled in a clinical study, and assessed its biological validity using a set of important pathways known to be involved in psoriasis. We also identified a key set of cytokines that are now strongly implicated in driving disease-related pathology, but which are not detected well on gene array platforms and require more sensitive methods to measure mRNA levels in skin tissues. Comparison of our transcriptome with three other published lists of psoriasis genes showed apparent inconsistencies based on the number of overlapping genes. We extended the well-established approach of Gene Set Enrichment Analysis (GSEA) to compare a new study with these other published list of differentially expressed genes (DEG) in a more comprehensive manner. We applied our method to these three published psoriasis transcriptomes and found them to be in good agreement with our study.<h4>Conclusions/significance</h4>Due to wide variability in clinical protocols, platform and sample handling, and subtle disease-related signals, intersection of published DEG lists was unable to establish consensus between studies. In order to leverage the power of multiple transcriptomes reported by several laboratories using different patients and protocols, more sophisticated methods like the extension of GSEA presented here, should be used in order to overcome the shortcomings of overlapping individual DEG approach.Mayte Suárez-FariñasMichelle A LowesLisa C ZabaJames G KruegerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 4, p e10247 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mayte Suárez-Fariñas Michelle A Lowes Lisa C Zaba James G Krueger Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA).
description	<h4>Background</h4>Our objective was to develop a consistent molecular definition of psoriasis. There have been several published microarray studies of psoriasis, and we compared disease-related genes identified across these different studies of psoriasis with our own in order to establish a consensus.<h4>Methodology/principal findings</h4>We present a psoriasis transcriptome from a group of 15 patients enrolled in a clinical study, and assessed its biological validity using a set of important pathways known to be involved in psoriasis. We also identified a key set of cytokines that are now strongly implicated in driving disease-related pathology, but which are not detected well on gene array platforms and require more sensitive methods to measure mRNA levels in skin tissues. Comparison of our transcriptome with three other published lists of psoriasis genes showed apparent inconsistencies based on the number of overlapping genes. We extended the well-established approach of Gene Set Enrichment Analysis (GSEA) to compare a new study with these other published list of differentially expressed genes (DEG) in a more comprehensive manner. We applied our method to these three published psoriasis transcriptomes and found them to be in good agreement with our study.<h4>Conclusions/significance</h4>Due to wide variability in clinical protocols, platform and sample handling, and subtle disease-related signals, intersection of published DEG lists was unable to establish consensus between studies. In order to leverage the power of multiple transcriptomes reported by several laboratories using different patients and protocols, more sophisticated methods like the extension of GSEA presented here, should be used in order to overcome the shortcomings of overlapping individual DEG approach.
format	article
author	Mayte Suárez-Fariñas Michelle A Lowes Lisa C Zaba James G Krueger
author_facet	Mayte Suárez-Fariñas Michelle A Lowes Lisa C Zaba James G Krueger
author_sort	Mayte Suárez-Fariñas
title	Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA).
title_short	Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA).
title_full	Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA).
title_fullStr	Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA).
title_full_unstemmed	Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA).
title_sort	evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (gsea).
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/9b137d3b41a24ffb9207d5d862ca68e7
work_keys_str_mv	AT maytesuarezfarinas evaluationofthepsoriasistranscriptomeacrossdifferentstudiesbygenesetenrichmentanalysisgsea AT michellealowes evaluationofthepsoriasistranscriptomeacrossdifferentstudiesbygenesetenrichmentanalysisgsea AT lisaczaba evaluationofthepsoriasistranscriptomeacrossdifferentstudiesbygenesetenrichmentanalysisgsea AT jamesgkrueger evaluationofthepsoriasistranscriptomeacrossdifferentstudiesbygenesetenrichmentanalysisgsea
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Evaluation of the psoriasis transcriptome across different studies by gene set enrichment analysis (GSEA).

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