Integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map.

Vast research efforts have been devoted to providing clinical diagnostic markers of myocardial infarction (MI), leading to over one million abstracts associated with "MI" and "Cardiovascular Diseases" in PubMed. Accumulation of the research results imposed a challenge to integrat...

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Autores principales:	Nguyen T Nguyen, Xiaolin Zhang, Cathy Wu, Richard A Lange, Robert J Chilton, Merry L Lindsey, Yu-Fang Jin
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/1860ed925c614e3e8c776aca563f55b1
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spelling	oai:doaj.org-article:1860ed925c614e3e8c776aca563f55b12021-11-18T05:53:04ZIntegrative computational and experimental approaches to establish a post-myocardial infarction knowledge map.1553-734X1553-735810.1371/journal.pcbi.1003472https://doaj.org/article/1860ed925c614e3e8c776aca563f55b12014-03-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24651374/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Vast research efforts have been devoted to providing clinical diagnostic markers of myocardial infarction (MI), leading to over one million abstracts associated with "MI" and "Cardiovascular Diseases" in PubMed. Accumulation of the research results imposed a challenge to integrate and interpret these results. To address this problem and better understand how the left ventricle (LV) remodels post-MI at both the molecular and cellular levels, we propose here an integrative framework that couples computational methods and experimental data. We selected an initial set of MI-related proteins from published human studies and constructed an MI-specific protein-protein-interaction network (MIPIN). Structural and functional analysis of the MIPIN showed that the post-MI LV exhibited increased representation of proteins involved in transcriptional activity, inflammatory response, and extracellular matrix (ECM) remodeling. Known plasma or serum expression changes of the MIPIN proteins in patients with MI were acquired by data mining of the PubMed and UniProt knowledgebase, and served as a training set to predict unlabeled MIPIN protein changes post-MI. The predictions were validated with published results in PubMed, suggesting prognosticative capability of the MIPIN. Further, we established the first knowledge map related to the post-MI response, providing a major step towards enhancing our understanding of molecular interactions specific to MI and linking the molecular interaction, cellular responses, and biological processes to quantify LV remodeling.Nguyen T NguyenXiaolin ZhangCathy WuRichard A LangeRobert J ChiltonMerry L LindseyYu-Fang JinPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 10, Iss 3, p e1003472 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Nguyen T Nguyen Xiaolin Zhang Cathy Wu Richard A Lange Robert J Chilton Merry L Lindsey Yu-Fang Jin Integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map.
description	Vast research efforts have been devoted to providing clinical diagnostic markers of myocardial infarction (MI), leading to over one million abstracts associated with "MI" and "Cardiovascular Diseases" in PubMed. Accumulation of the research results imposed a challenge to integrate and interpret these results. To address this problem and better understand how the left ventricle (LV) remodels post-MI at both the molecular and cellular levels, we propose here an integrative framework that couples computational methods and experimental data. We selected an initial set of MI-related proteins from published human studies and constructed an MI-specific protein-protein-interaction network (MIPIN). Structural and functional analysis of the MIPIN showed that the post-MI LV exhibited increased representation of proteins involved in transcriptional activity, inflammatory response, and extracellular matrix (ECM) remodeling. Known plasma or serum expression changes of the MIPIN proteins in patients with MI were acquired by data mining of the PubMed and UniProt knowledgebase, and served as a training set to predict unlabeled MIPIN protein changes post-MI. The predictions were validated with published results in PubMed, suggesting prognosticative capability of the MIPIN. Further, we established the first knowledge map related to the post-MI response, providing a major step towards enhancing our understanding of molecular interactions specific to MI and linking the molecular interaction, cellular responses, and biological processes to quantify LV remodeling.
format	article
author	Nguyen T Nguyen Xiaolin Zhang Cathy Wu Richard A Lange Robert J Chilton Merry L Lindsey Yu-Fang Jin
author_facet	Nguyen T Nguyen Xiaolin Zhang Cathy Wu Richard A Lange Robert J Chilton Merry L Lindsey Yu-Fang Jin
author_sort	Nguyen T Nguyen
title	Integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map.
title_short	Integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map.
title_full	Integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map.
title_fullStr	Integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map.
title_full_unstemmed	Integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map.
title_sort	integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/1860ed925c614e3e8c776aca563f55b1
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Integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map.

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