A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.

<h4>Background</h4>Alternative pre-mRNA splicing (AS) plays a central role in generating complex proteomes and influences development and disease. However, the regulation and etiology of AS in human tumorigenesis is not well understood.<h4>Methodology/principal findings</h4>A...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Chunjiang He, Fang Zhou, Zhixiang Zuo, Hanhua Cheng, Rongjia Zhou
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/68b160b1145a4a67938be563412cafd5
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:68b160b1145a4a67938be563412cafd5
record_format	dspace
spelling	oai:doaj.org-article:68b160b1145a4a67938be563412cafd52021-11-25T06:16:53ZA global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.1932-620310.1371/journal.pone.0004732https://doaj.org/article/68b160b1145a4a67938be563412cafd52009-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19266097/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Alternative pre-mRNA splicing (AS) plays a central role in generating complex proteomes and influences development and disease. However, the regulation and etiology of AS in human tumorigenesis is not well understood.<h4>Methodology/principal findings</h4>A Basic Local Alignment Search Tool database was constructed for the expressed sequence tags (ESTs) from all available databases of human cancer and normal tissues. An insertion or deletion in the alignment of EST/EST was used to identify alternatively spliced transcripts. Alignment of the ESTs with the genomic sequence was further used to confirm AS. Alternatively spliced transcripts in each tissue were then subtractively cross-screened to obtain tissue-specific variants. We systematically identified and characterized cancer/tissue-specific and alternatively spliced variants in the human genome based on a global view. We identified 15,093 cancer-specific variants of 9,989 genes from 27 types of human cancers and 14,376 normal tissue-specific variants of 7,240 genes from 35 normal tissues, which cover the main types of human tumors and normal tissues. Approximately 70% of these transcripts are novel. These data were integrated into a database HCSAS (http://202.114.72.39/database/human.html, pass:68756253). Moreover, we observed that the cancer-specific AS of both oncogenes and tumor suppressor genes are associated with specific cancer types. Cancer shows a preference in the selection of alternative splice-sites and utilization of alternative splicing types.<h4>Conclusions/significance</h4>These features of human cancer, together with the discovery of huge numbers of novel splice forms for cancer-associated genes, suggest an important and global role of cancer-specific AS during human tumorigenesis. We advise the use of cancer-specific alternative splicing as a potential source of new diagnostic, prognostic, predictive, and therapeutic tools for human cancer. The global view of cancer-specific AS is not only useful for exploring the complexity of the cancer transcriptome but also widens the eyeshot of clinical research.Chunjiang HeFang ZhouZhixiang ZuoHanhua ChengRongjia ZhouPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 4, Iss 3, p e4732 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Chunjiang He Fang Zhou Zhixiang Zuo Hanhua Cheng Rongjia Zhou A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.
description	<h4>Background</h4>Alternative pre-mRNA splicing (AS) plays a central role in generating complex proteomes and influences development and disease. However, the regulation and etiology of AS in human tumorigenesis is not well understood.<h4>Methodology/principal findings</h4>A Basic Local Alignment Search Tool database was constructed for the expressed sequence tags (ESTs) from all available databases of human cancer and normal tissues. An insertion or deletion in the alignment of EST/EST was used to identify alternatively spliced transcripts. Alignment of the ESTs with the genomic sequence was further used to confirm AS. Alternatively spliced transcripts in each tissue were then subtractively cross-screened to obtain tissue-specific variants. We systematically identified and characterized cancer/tissue-specific and alternatively spliced variants in the human genome based on a global view. We identified 15,093 cancer-specific variants of 9,989 genes from 27 types of human cancers and 14,376 normal tissue-specific variants of 7,240 genes from 35 normal tissues, which cover the main types of human tumors and normal tissues. Approximately 70% of these transcripts are novel. These data were integrated into a database HCSAS (http://202.114.72.39/database/human.html, pass:68756253). Moreover, we observed that the cancer-specific AS of both oncogenes and tumor suppressor genes are associated with specific cancer types. Cancer shows a preference in the selection of alternative splice-sites and utilization of alternative splicing types.<h4>Conclusions/significance</h4>These features of human cancer, together with the discovery of huge numbers of novel splice forms for cancer-associated genes, suggest an important and global role of cancer-specific AS during human tumorigenesis. We advise the use of cancer-specific alternative splicing as a potential source of new diagnostic, prognostic, predictive, and therapeutic tools for human cancer. The global view of cancer-specific AS is not only useful for exploring the complexity of the cancer transcriptome but also widens the eyeshot of clinical research.
format	article
author	Chunjiang He Fang Zhou Zhixiang Zuo Hanhua Cheng Rongjia Zhou
author_facet	Chunjiang He Fang Zhou Zhixiang Zuo Hanhua Cheng Rongjia Zhou
author_sort	Chunjiang He
title	A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.
title_short	A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.
title_full	A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.
title_fullStr	A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.
title_full_unstemmed	A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.
title_sort	global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/68b160b1145a4a67938be563412cafd5
work_keys_str_mv	AT chunjianghe aglobalviewofcancerspecifictranscriptvariantsbysubtractivetranscriptomewideanalysis AT fangzhou aglobalviewofcancerspecifictranscriptvariantsbysubtractivetranscriptomewideanalysis AT zhixiangzuo aglobalviewofcancerspecifictranscriptvariantsbysubtractivetranscriptomewideanalysis AT hanhuacheng aglobalviewofcancerspecifictranscriptvariantsbysubtractivetranscriptomewideanalysis AT rongjiazhou aglobalviewofcancerspecifictranscriptvariantsbysubtractivetranscriptomewideanalysis AT chunjianghe globalviewofcancerspecifictranscriptvariantsbysubtractivetranscriptomewideanalysis AT fangzhou globalviewofcancerspecifictranscriptvariantsbysubtractivetranscriptomewideanalysis AT zhixiangzuo globalviewofcancerspecifictranscriptvariantsbysubtractivetranscriptomewideanalysis AT hanhuacheng globalviewofcancerspecifictranscriptvariantsbysubtractivetranscriptomewideanalysis AT rongjiazhou globalviewofcancerspecifictranscriptvariantsbysubtractivetranscriptomewideanalysis
_version_	1718413988272799744

A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.

Ejemplares similares