Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package

Abstract Analyzing different omics data types independently is often too restrictive to allow for detection of subtle, but consistent, variations that are coherently supported based upon different assays. Integrating multi-omics data in one model can increase statistical power. However, designing su...
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Autor*in:	Sogand Sajedi [verfasserIn] Ghazal Ebrahimi [verfasserIn] Raheleh Roudi [verfasserIn] Isha Mehta [verfasserIn] Amirreza Heshmat [verfasserIn] Hanie Samimi [verfasserIn] Shiva Kazempour [verfasserIn] Aamir Zainulabadeen [verfasserIn] Thomas Roderick Docking [verfasserIn] Sukeshi Patel Arora [verfasserIn] Francisco Cigarroa [verfasserIn] Sudha Seshadri [verfasserIn] Aly Karsan [verfasserIn] Habil Zare [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Übergeordnetes Werk:	In: Scientific Reports - Nature Portfolio, 2011, 13(2023), 1, Seite 10
Übergeordnetes Werk:	volume:13 ; year:2023 ; number:1 ; pages:10

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1038/s41598-023-48237-8

Katalog-ID:	DOAJ099884607

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allfields	10.1038/s41598-023-48237-8 doi (DE-627)DOAJ099884607 (DE-599)DOAJ46004c6c5edd4eae922198954ba955dd DE-627 ger DE-627 rakwb eng Sogand Sajedi verfasserin aut Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Analyzing different omics data types independently is often too restrictive to allow for detection of subtle, but consistent, variations that are coherently supported based upon different assays. Integrating multi-omics data in one model can increase statistical power. However, designing such a model is challenging because different omics are measured at different levels. We developed the iNETgrate package ( https://bioconductor.org/packages/iNETgrate/ ) that efficiently integrates transcriptome and DNA methylation data in a single gene network. Applying iNETgrate on five independent datasets improved prognostication compared to common clinical gold standards and a patient similarity network approach. Medicine R Science Q Ghazal Ebrahimi verfasserin aut Raheleh Roudi verfasserin aut Isha Mehta verfasserin aut Amirreza Heshmat verfasserin aut Hanie Samimi verfasserin aut Shiva Kazempour verfasserin aut Aamir Zainulabadeen verfasserin aut Thomas Roderick Docking verfasserin aut Sukeshi Patel Arora verfasserin aut Francisco Cigarroa verfasserin aut Sudha Seshadri verfasserin aut Aly Karsan verfasserin aut Habil Zare verfasserin aut In Scientific Reports Nature Portfolio, 2011 13(2023), 1, Seite 10 (DE-627)663366712 (DE-600)2615211-3 20452322 nnns volume:13 year:2023 number:1 pages:10 https://doi.org/10.1038/s41598-023-48237-8 kostenfrei https://doaj.org/article/46004c6c5edd4eae922198954ba955dd kostenfrei https://doi.org/10.1038/s41598-023-48237-8 kostenfrei https://doaj.org/toc/2045-2322 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_381 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023 1 10
spelling	10.1038/s41598-023-48237-8 doi (DE-627)DOAJ099884607 (DE-599)DOAJ46004c6c5edd4eae922198954ba955dd DE-627 ger DE-627 rakwb eng Sogand Sajedi verfasserin aut Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Analyzing different omics data types independently is often too restrictive to allow for detection of subtle, but consistent, variations that are coherently supported based upon different assays. Integrating multi-omics data in one model can increase statistical power. However, designing such a model is challenging because different omics are measured at different levels. We developed the iNETgrate package ( https://bioconductor.org/packages/iNETgrate/ ) that efficiently integrates transcriptome and DNA methylation data in a single gene network. Applying iNETgrate on five independent datasets improved prognostication compared to common clinical gold standards and a patient similarity network approach. Medicine R Science Q Ghazal Ebrahimi verfasserin aut Raheleh Roudi verfasserin aut Isha Mehta verfasserin aut Amirreza Heshmat verfasserin aut Hanie Samimi verfasserin aut Shiva Kazempour verfasserin aut Aamir Zainulabadeen verfasserin aut Thomas Roderick Docking verfasserin aut Sukeshi Patel Arora verfasserin aut Francisco Cigarroa verfasserin aut Sudha Seshadri verfasserin aut Aly Karsan verfasserin aut Habil Zare verfasserin aut In Scientific Reports Nature Portfolio, 2011 13(2023), 1, Seite 10 (DE-627)663366712 (DE-600)2615211-3 20452322 nnns volume:13 year:2023 number:1 pages:10 https://doi.org/10.1038/s41598-023-48237-8 kostenfrei https://doaj.org/article/46004c6c5edd4eae922198954ba955dd kostenfrei https://doi.org/10.1038/s41598-023-48237-8 kostenfrei https://doaj.org/toc/2045-2322 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_381 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023 1 10
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allfieldsSound	10.1038/s41598-023-48237-8 doi (DE-627)DOAJ099884607 (DE-599)DOAJ46004c6c5edd4eae922198954ba955dd DE-627 ger DE-627 rakwb eng Sogand Sajedi verfasserin aut Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Analyzing different omics data types independently is often too restrictive to allow for detection of subtle, but consistent, variations that are coherently supported based upon different assays. Integrating multi-omics data in one model can increase statistical power. However, designing such a model is challenging because different omics are measured at different levels. We developed the iNETgrate package ( https://bioconductor.org/packages/iNETgrate/ ) that efficiently integrates transcriptome and DNA methylation data in a single gene network. Applying iNETgrate on five independent datasets improved prognostication compared to common clinical gold standards and a patient similarity network approach. Medicine R Science Q Ghazal Ebrahimi verfasserin aut Raheleh Roudi verfasserin aut Isha Mehta verfasserin aut Amirreza Heshmat verfasserin aut Hanie Samimi verfasserin aut Shiva Kazempour verfasserin aut Aamir Zainulabadeen verfasserin aut Thomas Roderick Docking verfasserin aut Sukeshi Patel Arora verfasserin aut Francisco Cigarroa verfasserin aut Sudha Seshadri verfasserin aut Aly Karsan verfasserin aut Habil Zare verfasserin aut In Scientific Reports Nature Portfolio, 2011 13(2023), 1, Seite 10 (DE-627)663366712 (DE-600)2615211-3 20452322 nnns volume:13 year:2023 number:1 pages:10 https://doi.org/10.1038/s41598-023-48237-8 kostenfrei https://doaj.org/article/46004c6c5edd4eae922198954ba955dd kostenfrei https://doi.org/10.1038/s41598-023-48237-8 kostenfrei https://doaj.org/toc/2045-2322 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_381 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2023 1 10
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spellingShingle	Sogand Sajedi misc Medicine misc R misc Science misc Q Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package
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topic_title	Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package
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title	Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package
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author_browse	Sogand Sajedi Ghazal Ebrahimi Raheleh Roudi Isha Mehta Amirreza Heshmat Hanie Samimi Shiva Kazempour Aamir Zainulabadeen Thomas Roderick Docking Sukeshi Patel Arora Francisco Cigarroa Sudha Seshadri Aly Karsan Habil Zare
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title_sort	integrating dna methylation and gene expression data in a single gene network using the inetgrate package
title_auth	Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package
abstract	Abstract Analyzing different omics data types independently is often too restrictive to allow for detection of subtle, but consistent, variations that are coherently supported based upon different assays. Integrating multi-omics data in one model can increase statistical power. However, designing such a model is challenging because different omics are measured at different levels. We developed the iNETgrate package ( https://bioconductor.org/packages/iNETgrate/ ) that efficiently integrates transcriptome and DNA methylation data in a single gene network. Applying iNETgrate on five independent datasets improved prognostication compared to common clinical gold standards and a patient similarity network approach.
abstractGer	Abstract Analyzing different omics data types independently is often too restrictive to allow for detection of subtle, but consistent, variations that are coherently supported based upon different assays. Integrating multi-omics data in one model can increase statistical power. However, designing such a model is challenging because different omics are measured at different levels. We developed the iNETgrate package ( https://bioconductor.org/packages/iNETgrate/ ) that efficiently integrates transcriptome and DNA methylation data in a single gene network. Applying iNETgrate on five independent datasets improved prognostication compared to common clinical gold standards and a patient similarity network approach.
abstract_unstemmed	Abstract Analyzing different omics data types independently is often too restrictive to allow for detection of subtle, but consistent, variations that are coherently supported based upon different assays. Integrating multi-omics data in one model can increase statistical power. However, designing such a model is challenging because different omics are measured at different levels. We developed the iNETgrate package ( https://bioconductor.org/packages/iNETgrate/ ) that efficiently integrates transcriptome and DNA methylation data in a single gene network. Applying iNETgrate on five independent datasets improved prognostication compared to common clinical gold standards and a patient similarity network approach.
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title_short	Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package
url	https://doi.org/10.1038/s41598-023-48237-8 https://doaj.org/article/46004c6c5edd4eae922198954ba955dd https://doaj.org/toc/2045-2322
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author2	Ghazal Ebrahimi Raheleh Roudi Isha Mehta Amirreza Heshmat Hanie Samimi Shiva Kazempour Aamir Zainulabadeen Thomas Roderick Docking Sukeshi Patel Arora Francisco Cigarroa Sudha Seshadri Aly Karsan Habil Zare
author2Str	Ghazal Ebrahimi Raheleh Roudi Isha Mehta Amirreza Heshmat Hanie Samimi Shiva Kazempour Aamir Zainulabadeen Thomas Roderick Docking Sukeshi Patel Arora Francisco Cigarroa Sudha Seshadri Aly Karsan Habil Zare
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Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package

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