Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map

Nguyen T. Nguyen, Xiaolin Zhang, Cathy Wu, Richard A. Lange, Robert J. Chilton, Merry L. Lindsey, Yu Fang Jin

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article numbere1003472
JournalPLoS computational biology
Volume10
Issue number3
DOIs
StatePublished - Mar 2014

Fingerprint

Myocardial Infarction
myocardial infarction
Proteins
Protein Interaction Maps
protein
Protein Interaction Networks
protein-protein interactions
Protein-protein Interaction
Left Ventricle
PubMed
Protein
Remodeling
Heart Ventricles
Molecular interactions
proteins
Knowledge
Biological Phenomena
Ventricular Remodeling
Data Mining
Knowledge Bases

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Ecology
  • Molecular Biology
  • Genetics
  • Cellular and Molecular Neuroscience
  • Computational Theory and Mathematics

Cite this

Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map. / Nguyen, Nguyen T.; Zhang, Xiaolin; Wu, Cathy; Lange, Richard A.; Chilton, Robert J.; Lindsey, Merry L.; Jin, Yu Fang.

In: PLoS computational biology, Vol. 10, No. 3, e1003472, 03.2014.

Research output: Contribution to journalArticle

Nguyen, Nguyen T. ; Zhang, Xiaolin ; Wu, Cathy ; Lange, Richard A. ; Chilton, Robert J. ; Lindsey, Merry L. ; Jin, Yu Fang. / Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map. In: PLoS computational biology. 2014 ; Vol. 10, No. 3.
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