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Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data

BACKGROUND: Prostate cancer (PCa) is a leading cause of cancer-related death of men worldwide. There is an urgent need to develop novel biomarkers for PCa prognosis and diagnosis in the post prostate-specific antigen era. Long intergenic noncoding RNAs (lincRNAs) play essential roles in many physiol...

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Autores principales: Cui, Weirong, Qian, Yulan, Zhou, Xiaoke, Lin, Yuxin, Jiang, Junfeng, Chen, Jiajia, Zhao, Zhongming, Shen, Bairong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4474418/
https://www.ncbi.nlm.nih.gov/pubmed/26100580
http://dx.doi.org/10.1186/1471-2164-16-S7-S3
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author Cui, Weirong
Qian, Yulan
Zhou, Xiaoke
Lin, Yuxin
Jiang, Junfeng
Chen, Jiajia
Zhao, Zhongming
Shen, Bairong
author_facet Cui, Weirong
Qian, Yulan
Zhou, Xiaoke
Lin, Yuxin
Jiang, Junfeng
Chen, Jiajia
Zhao, Zhongming
Shen, Bairong
author_sort Cui, Weirong
collection PubMed
description BACKGROUND: Prostate cancer (PCa) is a leading cause of cancer-related death of men worldwide. There is an urgent need to develop novel biomarkers for PCa prognosis and diagnosis in the post prostate-specific antigen era. Long intergenic noncoding RNAs (lincRNAs) play essential roles in many physiological processes and can serve as alternative biomarkers for prostate cancer, but there has been no systematic investigation of lincRNAs in PCa yet. RESULTS: Nine lincRNA co-expression modules were identified from PCa RNA-Seq data. The association between the principle component of each module and the PCa phenotype was examined by calculating the Pearson's correlation coefficients. Three modules (M1, M3, and M5) were found associated with PCa. Two modules (M3 and M5) were significantly enriched with lincRNAs, and one of them, M3, may be used as a lincRNA module-biomarker for PCa diagnosis. This module includes seven essential lincRNAs: TCONS_l2_00001418, TCONS_l2_00008237, TCONS_l2_00011130, TCONS_l2_00013175, TCONS_l2_00022611, TCONS_l2_00022670 and linc-PXN-1. The clustering analysis and microRNA enrichment analysis further confirmed our findings. CONCLUSION: The correlation between lincRNAs and protein-coding genes is helpful for further exploration of functional mechanisms of lincRNAs in PCa. This study provides some important insights into the roles of lincRNAs in PCa and suggests a few lincRNAs as candidate biomarkers for PCa diagnosis and prognosis.
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spelling pubmed-44744182015-06-25 Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data Cui, Weirong Qian, Yulan Zhou, Xiaoke Lin, Yuxin Jiang, Junfeng Chen, Jiajia Zhao, Zhongming Shen, Bairong BMC Genomics Research BACKGROUND: Prostate cancer (PCa) is a leading cause of cancer-related death of men worldwide. There is an urgent need to develop novel biomarkers for PCa prognosis and diagnosis in the post prostate-specific antigen era. Long intergenic noncoding RNAs (lincRNAs) play essential roles in many physiological processes and can serve as alternative biomarkers for prostate cancer, but there has been no systematic investigation of lincRNAs in PCa yet. RESULTS: Nine lincRNA co-expression modules were identified from PCa RNA-Seq data. The association between the principle component of each module and the PCa phenotype was examined by calculating the Pearson's correlation coefficients. Three modules (M1, M3, and M5) were found associated with PCa. Two modules (M3 and M5) were significantly enriched with lincRNAs, and one of them, M3, may be used as a lincRNA module-biomarker for PCa diagnosis. This module includes seven essential lincRNAs: TCONS_l2_00001418, TCONS_l2_00008237, TCONS_l2_00011130, TCONS_l2_00013175, TCONS_l2_00022611, TCONS_l2_00022670 and linc-PXN-1. The clustering analysis and microRNA enrichment analysis further confirmed our findings. CONCLUSION: The correlation between lincRNAs and protein-coding genes is helpful for further exploration of functional mechanisms of lincRNAs in PCa. This study provides some important insights into the roles of lincRNAs in PCa and suggests a few lincRNAs as candidate biomarkers for PCa diagnosis and prognosis. BioMed Central 2015-06-11 /pmc/articles/PMC4474418/ /pubmed/26100580 http://dx.doi.org/10.1186/1471-2164-16-S7-S3 Text en Copyright © 2015 Cui et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Cui, Weirong
Qian, Yulan
Zhou, Xiaoke
Lin, Yuxin
Jiang, Junfeng
Chen, Jiajia
Zhao, Zhongming
Shen, Bairong
Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data
title Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data
title_full Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data
title_fullStr Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data
title_full_unstemmed Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data
title_short Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data
title_sort discovery and characterization of long intergenic non-coding rnas (lincrna) module biomarkers in prostate cancer: an integrative analysis of rna-seq data
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4474418/
https://www.ncbi.nlm.nih.gov/pubmed/26100580
http://dx.doi.org/10.1186/1471-2164-16-S7-S3
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