Analyzing cancer gene expression data through the lens of normal tissue-specificity.

The genetic alterations that underlie cancer development are highly tissue-specific with the majority of driving alterations occurring in only a few cancer types and with alterations common to multiple cancer types often showing a tissue-specific functional impact. This tissue-specificity means that...

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Autor principal:	H Robert Frost
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/b742e38ba5a742f3a30e5d4194890e57
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spelling	oai:doaj.org-article:b742e38ba5a742f3a30e5d4194890e572021-11-25T05:40:36ZAnalyzing cancer gene expression data through the lens of normal tissue-specificity.1553-734X1553-735810.1371/journal.pcbi.1009085https://doaj.org/article/b742e38ba5a742f3a30e5d4194890e572021-06-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009085https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The genetic alterations that underlie cancer development are highly tissue-specific with the majority of driving alterations occurring in only a few cancer types and with alterations common to multiple cancer types often showing a tissue-specific functional impact. This tissue-specificity means that the biology of normal tissues carries important information regarding the pathophysiology of the associated cancers, information that can be leveraged to improve the power and accuracy of cancer genomic analyses. Research exploring the use of normal tissue data for the analysis of cancer genomics has primarily focused on the paired analysis of tumor and adjacent normal samples. Efforts to leverage the general characteristics of normal tissue for cancer analysis has received less attention with most investigations focusing on understanding the tissue-specific factors that lead to individual genomic alterations or dysregulated pathways within a single cancer type. To address this gap and support scenarios where adjacent normal tissue samples are not available, we explored the genome-wide association between the transcriptomes of 21 solid human cancers and their associated normal tissues as profiled in healthy individuals. While the average gene expression profiles of normal and cancerous tissue may appear distinct, with normal tissues more similar to other normal tissues than to the associated cancer types, when transformed into relative expression values, i.e., the ratio of expression in one tissue or cancer relative to the mean in other tissues or cancers, the close association between gene activity in normal tissues and related cancers is revealed. As we demonstrate through an analysis of tumor data from The Cancer Genome Atlas and normal tissue data from the Human Protein Atlas, this association between tissue-specific and cancer-specific expression values can be leveraged to improve the prognostic modeling of cancer, the comparative analysis of different cancer types, and the analysis of cancer and normal tissue pairs.H Robert FrostPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 6, p e1009085 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 H Robert Frost Analyzing cancer gene expression data through the lens of normal tissue-specificity.
description	The genetic alterations that underlie cancer development are highly tissue-specific with the majority of driving alterations occurring in only a few cancer types and with alterations common to multiple cancer types often showing a tissue-specific functional impact. This tissue-specificity means that the biology of normal tissues carries important information regarding the pathophysiology of the associated cancers, information that can be leveraged to improve the power and accuracy of cancer genomic analyses. Research exploring the use of normal tissue data for the analysis of cancer genomics has primarily focused on the paired analysis of tumor and adjacent normal samples. Efforts to leverage the general characteristics of normal tissue for cancer analysis has received less attention with most investigations focusing on understanding the tissue-specific factors that lead to individual genomic alterations or dysregulated pathways within a single cancer type. To address this gap and support scenarios where adjacent normal tissue samples are not available, we explored the genome-wide association between the transcriptomes of 21 solid human cancers and their associated normal tissues as profiled in healthy individuals. While the average gene expression profiles of normal and cancerous tissue may appear distinct, with normal tissues more similar to other normal tissues than to the associated cancer types, when transformed into relative expression values, i.e., the ratio of expression in one tissue or cancer relative to the mean in other tissues or cancers, the close association between gene activity in normal tissues and related cancers is revealed. As we demonstrate through an analysis of tumor data from The Cancer Genome Atlas and normal tissue data from the Human Protein Atlas, this association between tissue-specific and cancer-specific expression values can be leveraged to improve the prognostic modeling of cancer, the comparative analysis of different cancer types, and the analysis of cancer and normal tissue pairs.
format	article
author	H Robert Frost
author_facet	H Robert Frost
author_sort	H Robert Frost
title	Analyzing cancer gene expression data through the lens of normal tissue-specificity.
title_short	Analyzing cancer gene expression data through the lens of normal tissue-specificity.
title_full	Analyzing cancer gene expression data through the lens of normal tissue-specificity.
title_fullStr	Analyzing cancer gene expression data through the lens of normal tissue-specificity.
title_full_unstemmed	Analyzing cancer gene expression data through the lens of normal tissue-specificity.
title_sort	analyzing cancer gene expression data through the lens of normal tissue-specificity.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/b742e38ba5a742f3a30e5d4194890e57
work_keys_str_mv	AT hrobertfrost analyzingcancergeneexpressiondatathroughthelensofnormaltissuespecificity
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Analyzing cancer gene expression data through the lens of normal tissue-specificity.

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