Phrase mining of textual data to analyze extracellular matrix protein patterns across cardiovascular disease

American Journal of Physiology. Heart and Circulatory Physiology
David A LiemJiaWei Han

Abstract

Extracellular matrix (ECM) proteins have been shown to play important roles regulating multiple biological processes in an array of organ systems, including the cardiovascular system. Using a novel bioinformatics text-mining tool, we studied six categories of cardiovascular disease (CVD), namely, ischemic heart disease, cardiomyopathies, cerebrovascular accident, congenital heart disease, arrhythmias, and valve disease, anticipating novel ECM protein-disease and protein-protein relationships hidden within vast quantities of textual data. We conducted a phrase-mining analysis, delineating the relationships of 709 ECM proteins with the 6 groups of CVDs reported in 1,099,254 abstracts. The technology pipeline known as Context-Aware Semantic Online Analytical Processing was applied to semantically rank the association of proteins to each CVD and all six CVDs, performing analyses to quantify each protein-disease relationship. We performed principal component analysis and hierarchical clustering of the data, where each protein was visualized as a six-dimensional vector. We found that ECM proteins display variable degrees of association with the six CVDs; certain CVDs share groups of associated proteins, whereas others have divergent ...Continue Reading

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Citations

Sep 22, 2018·American Journal of Physiology. Heart and Circulatory Physiology·Maria BloksgaardLuis A Martinez-Lemus
Jan 31, 2019·Genes·Bilal MirzaPeipei Ping
Dec 6, 2019·Briefings in Bioinformatics·Bohdan B KhomtchoukThemistocles L Assimes
Dec 18, 2019·Pharmacological Reviews·Jhana O HendrickxStuart Maudsley
Mar 23, 2021·Cardiovascular Research·J Harry CaufieldPeipei Ping
Sep 27, 2018·Journal of Proteome Research·Edward LauMaggie P Y Lam

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Methods Mentioned

BETA
PCA
GTPase
glycosylation
GTPases
imaging techniques

Software Mentioned

Learn
Pandas
Python
SciKit
Reactome analysis
CaseOLAP Online Analytical Processing
R
MatrixDB
Reactome
Pandas package

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