On the reproducibility of TCGA ovarian cancer microRNA profiles.

Dysregulated microRNA (miRNA) expression is a well-established feature of human cancer. However, the role of specific miRNAs in determining cancer outcomes remains unclear. Using Level 3 expression data from the Cancer Genome Atlas (TCGA), we identified 61 miRNAs that are associated with overall sur...

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Autores principales:	Ying-Wooi Wan, Claire M Mach, Genevera I Allen, Matthew L Anderson, Zhandong Liu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e4f42d26f60b46e1b62c7d9d37cae51e
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spelling	oai:doaj.org-article:e4f42d26f60b46e1b62c7d9d37cae51e2021-11-18T08:34:56ZOn the reproducibility of TCGA ovarian cancer microRNA profiles.1932-620310.1371/journal.pone.0087782https://doaj.org/article/e4f42d26f60b46e1b62c7d9d37cae51e2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24489963/?tool=EBIhttps://doaj.org/toc/1932-6203Dysregulated microRNA (miRNA) expression is a well-established feature of human cancer. However, the role of specific miRNAs in determining cancer outcomes remains unclear. Using Level 3 expression data from the Cancer Genome Atlas (TCGA), we identified 61 miRNAs that are associated with overall survival in 469 ovarian cancers profiled by microarray (p<0.01). We also identified 12 miRNAs that are associated with survival when miRNAs were profiled in the same specimens using Next Generation Sequencing (miRNA-Seq) (p<0.01). Surprisingly, only 1 miRNA transcript is associated with ovarian cancer survival in both datasets. Our analyses indicate that this discrepancy is due to the fact that miRNA levels reported by the two platforms correlate poorly, even after correcting for potential issues inherent to signal detection algorithms. Corrections for false discovery and microRNA abundance had minimal impact on this discrepancy. Further investigation is warranted.Ying-Wooi WanClaire M MachGenevera I AllenMatthew L AndersonZhandong LiuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 1, p e87782 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ying-Wooi Wan Claire M Mach Genevera I Allen Matthew L Anderson Zhandong Liu On the reproducibility of TCGA ovarian cancer microRNA profiles.
description	Dysregulated microRNA (miRNA) expression is a well-established feature of human cancer. However, the role of specific miRNAs in determining cancer outcomes remains unclear. Using Level 3 expression data from the Cancer Genome Atlas (TCGA), we identified 61 miRNAs that are associated with overall survival in 469 ovarian cancers profiled by microarray (p<0.01). We also identified 12 miRNAs that are associated with survival when miRNAs were profiled in the same specimens using Next Generation Sequencing (miRNA-Seq) (p<0.01). Surprisingly, only 1 miRNA transcript is associated with ovarian cancer survival in both datasets. Our analyses indicate that this discrepancy is due to the fact that miRNA levels reported by the two platforms correlate poorly, even after correcting for potential issues inherent to signal detection algorithms. Corrections for false discovery and microRNA abundance had minimal impact on this discrepancy. Further investigation is warranted.
format	article
author	Ying-Wooi Wan Claire M Mach Genevera I Allen Matthew L Anderson Zhandong Liu
author_facet	Ying-Wooi Wan Claire M Mach Genevera I Allen Matthew L Anderson Zhandong Liu
author_sort	Ying-Wooi Wan
title	On the reproducibility of TCGA ovarian cancer microRNA profiles.
title_short	On the reproducibility of TCGA ovarian cancer microRNA profiles.
title_full	On the reproducibility of TCGA ovarian cancer microRNA profiles.
title_fullStr	On the reproducibility of TCGA ovarian cancer microRNA profiles.
title_full_unstemmed	On the reproducibility of TCGA ovarian cancer microRNA profiles.
title_sort	on the reproducibility of tcga ovarian cancer microrna profiles.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/e4f42d26f60b46e1b62c7d9d37cae51e
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On the reproducibility of TCGA ovarian cancer microRNA profiles.

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