Integrated exon level expression analysis of driver genes explain their role in colorectal cancer.

Integrated analysis of genomic and transcriptomic level changes holds promise for a better understanding of colorectal cancer (CRC) biology. There is a pertinent need to explain the functional effect of genome level changes by integrating the information at the transcript level. Using high resolutio...

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Autores principales:	Mohammad Azhar Aziz, Sathish Periyasamy, Zeyad Al Yousef, Ibrahim AlAbdulkarim, Majed Al Otaibi, Abdulaziz Alfahed, Glowi Alasiri
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cc13a20360bc41bbb0446401f3b178a2
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spelling	oai:doaj.org-article:cc13a20360bc41bbb0446401f3b178a22021-11-25T05:55:39ZIntegrated exon level expression analysis of driver genes explain their role in colorectal cancer.1932-620310.1371/journal.pone.0110134https://doaj.org/article/cc13a20360bc41bbb0446401f3b178a22014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0110134https://doaj.org/toc/1932-6203Integrated analysis of genomic and transcriptomic level changes holds promise for a better understanding of colorectal cancer (CRC) biology. There is a pertinent need to explain the functional effect of genome level changes by integrating the information at the transcript level. Using high resolution cytogenetics array, we had earlier identified driver genes by 'Genomic Identification of Significant Targets In Cancer (GISTIC)' analysis of paired tumour-normal samples from colorectal cancer patients. In this study, we analyze these driver genes at three levels using exon array data--gene, exon and network. Gene level analysis revealed a small subset to experience differential expression. These results were reinforced by carrying out separate differential expression analyses (SAM and LIMMA). ATP8B1 was found to be the novel gene associated with CRC that shows changes at cytogenetic, gene and exon levels. Splice index of 29 exons corresponding to 13 genes was found to be significantly altered in tumour samples. Driver genes were used to construct regulatory networks for tumour and normal groups. There were rearrangements in transcription factor genes suggesting the presence of regulatory switching. The regulatory pattern of AHR gene was found to have the most significant alteration. Our results integrate data with focus on driver genes resulting in highly enriched novel molecules that need further studies to establish their role in CRC.Mohammad Azhar AzizSathish PeriyasamyZeyad Al YousefIbrahim AlAbdulkarimMajed Al OtaibiAbdulaziz AlfahedGlowi AlasiriPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 10, p e110134 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mohammad Azhar Aziz Sathish Periyasamy Zeyad Al Yousef Ibrahim AlAbdulkarim Majed Al Otaibi Abdulaziz Alfahed Glowi Alasiri Integrated exon level expression analysis of driver genes explain their role in colorectal cancer.
description	Integrated analysis of genomic and transcriptomic level changes holds promise for a better understanding of colorectal cancer (CRC) biology. There is a pertinent need to explain the functional effect of genome level changes by integrating the information at the transcript level. Using high resolution cytogenetics array, we had earlier identified driver genes by 'Genomic Identification of Significant Targets In Cancer (GISTIC)' analysis of paired tumour-normal samples from colorectal cancer patients. In this study, we analyze these driver genes at three levels using exon array data--gene, exon and network. Gene level analysis revealed a small subset to experience differential expression. These results were reinforced by carrying out separate differential expression analyses (SAM and LIMMA). ATP8B1 was found to be the novel gene associated with CRC that shows changes at cytogenetic, gene and exon levels. Splice index of 29 exons corresponding to 13 genes was found to be significantly altered in tumour samples. Driver genes were used to construct regulatory networks for tumour and normal groups. There were rearrangements in transcription factor genes suggesting the presence of regulatory switching. The regulatory pattern of AHR gene was found to have the most significant alteration. Our results integrate data with focus on driver genes resulting in highly enriched novel molecules that need further studies to establish their role in CRC.
format	article
author	Mohammad Azhar Aziz Sathish Periyasamy Zeyad Al Yousef Ibrahim AlAbdulkarim Majed Al Otaibi Abdulaziz Alfahed Glowi Alasiri
author_facet	Mohammad Azhar Aziz Sathish Periyasamy Zeyad Al Yousef Ibrahim AlAbdulkarim Majed Al Otaibi Abdulaziz Alfahed Glowi Alasiri
author_sort	Mohammad Azhar Aziz
title	Integrated exon level expression analysis of driver genes explain their role in colorectal cancer.
title_short	Integrated exon level expression analysis of driver genes explain their role in colorectal cancer.
title_full	Integrated exon level expression analysis of driver genes explain their role in colorectal cancer.
title_fullStr	Integrated exon level expression analysis of driver genes explain their role in colorectal cancer.
title_full_unstemmed	Integrated exon level expression analysis of driver genes explain their role in colorectal cancer.
title_sort	integrated exon level expression analysis of driver genes explain their role in colorectal cancer.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/cc13a20360bc41bbb0446401f3b178a2
work_keys_str_mv	AT mohammadazharaziz integratedexonlevelexpressionanalysisofdrivergenesexplaintheirroleincolorectalcancer AT sathishperiyasamy integratedexonlevelexpressionanalysisofdrivergenesexplaintheirroleincolorectalcancer AT zeyadalyousef integratedexonlevelexpressionanalysisofdrivergenesexplaintheirroleincolorectalcancer AT ibrahimalabdulkarim integratedexonlevelexpressionanalysisofdrivergenesexplaintheirroleincolorectalcancer AT majedalotaibi integratedexonlevelexpressionanalysisofdrivergenesexplaintheirroleincolorectalcancer AT abdulazizalfahed integratedexonlevelexpressionanalysisofdrivergenesexplaintheirroleincolorectalcancer AT glowialasiri integratedexonlevelexpressionanalysisofdrivergenesexplaintheirroleincolorectalcancer
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Integrated exon level expression analysis of driver genes explain their role in colorectal cancer.

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