Journal Article
. 2020 Jun; 11:483.
doi: 10.3389/fphys.2020.00483.

Identification of Post-myocardial Infarction Blood Expression Signatures Using Multiple Feature Selection Strategies

Ming Li 1 Fuli Chen 2 Yaling Zhang 3 Yan Xiong 2 Qiyong Li 2 Hui Huang 2 
  • PMID: 32581823
  •     75 References
  •     1 citations


Myocardial infarction (MI) is a type of serious heart attack in which the blood flow to the heart is suddenly interrupted, resulting in injury to the heart muscles due to a lack of oxygen supply. Although clinical diagnosis methods can be used to identify the occurrence of MI, using the changes of molecular markers or characteristic molecules in blood to characterize the early phase and later trend of MI will help us choose a more reasonable treatment plan. Previously, comparative transcriptome studies focused on finding differentially expressed genes between MI patients and healthy people. However, signature molecules altered in different phases of MI have not been well excavated. We developed a set of computational approaches integrating multiple machine learning algorithms, including Monte Carlo feature selection (MCFS), incremental feature selection (IFS), and support vector machine (SVM), to identify gene expression characteristics on different phases of MI. 134 genes were determined to serve as features for building optimal SVM classifiers to distinguish acute MI and post-MI. Subsequently, functional enrichment analyses followed by protein-protein interaction analysis on 134 genes identified several hub genes (IL1R1, TLR2, and TLR4) associated with progression of MI, which can be used as new diagnostic molecules for MI.

Keywords: Monte Carlo feature selection; gene; incremental feature selection; myocardial infarction; support vector machine.

Ischemic preconditioning-mediated cardioprotection is disrupted in heterozygous Flt-1 (VEGFR-1) knockout mice.
Sankar Addya, Keisuke Shiroto, +8 authors, Nilanjana Maulik.
J Mol Cell Cardiol, 2005 Feb 09; 38(2). PMID: 15698841
Bioinformatic screening for key miRNAs and genes associated with myocardial infarction.
Ke Wu, Qiang Zhao, +4 authors, Quanming Zhao.
FEBS Open Bio, 2018 Jun 22; 8(6). PMID: 29928570    Free PMC article.
Differences between men and women in terms of clinical features of ST-segment elevation acute myocardial infarction.
Masami Kosuge, Kazuo Kimura, +12 authors, Satoshi Umemura.
Circ J, 2006 Feb 28; 70(3). PMID: 16501283
Release of fatty acid-binding protein from isolated rat heart subjected to ischemia and reperfusion or to the calcium paradox.
J F Glatz, M van Bilsen, +3 authors, R S Reneman.
Biochim Biophys Acta, 1988 Jul 01; 961(1). PMID: 3260112
Serum levels of the interleukin-1 receptor family member ST2 predict mortality and clinical outcome in acute myocardial infarction.
Masahisa Shimpo, David A Morrow, +4 authors, Richard T Lee.
Circulation, 2004 May 01; 109(18). PMID: 15117853
Highly Cited.
A novel autosomal dominant condition consisting of congenital heart defects and low atrial rhythm maps to chromosome 9q.
Judith B A van de Meerakker, Klaartje van Engelen, +8 authors, Alex V Postma.
Eur J Hum Genet, 2011 Mar 10; 19(7). PMID: 21386876    Free PMC article.
The cardioprotection of the insulin-mediated PI3K/Akt/mTOR signaling pathway.
Hong Yao, Xiangyang Han, Xiuzhen Han.
Am J Cardiovasc Drugs, 2014 Aug 28; 14(6). PMID: 25160498
Peripheral Blood RNA Levels of QSOX1 and PLBD1 Are New Independent Predictors of Left Ventricular Dysfunction After Acute Myocardial Infarction.
Maarten Vanhaverbeke, Mélanie Vausort, +11 authors, EU-CardioRNA COST Action CA17129.
Circ Genom Precis Med, 2019 Nov 23; 12(12). PMID: 31756302    Free PMC article.
Investigating the gene expression profiles of cells in seven embryonic stages with machine learning algorithms.
Lei Chen, XiaoYong Pan, +5 authors, Yu-Dong Cai.
Genomics, 2020 Feb 12; 112(3). PMID: 32045671
Glycogen phosphorylase isoenzyme BB to diagnose ischaemic myocardial damage.
J Mair.
Clin Chim Acta, 1998 May 15; 272(1). PMID: 9581859
Inhibition of RIP1-dependent necrosis prevents adverse cardiac remodeling after myocardial ischemia-reperfusion in vivo.
Martinus I F J Oerlemans, Jia Liu, +4 authors, Joost P G Sluijter.
Basic Res Cardiol, 2012 May 04; 107(4). PMID: 22553001
Highly Cited.
Identification of key genes involved in myocardial infarction.
Linlin Qiu, Xueqing Liu.
Eur J Med Res, 2019 Jul 05; 24(1). PMID: 31269974    Free PMC article.
Anti-apolipoprotein A-1 IgG in patients with myocardial infarction promotes inflammation through TLR2/CD14 complex.
S Pagano, N Satta, +6 authors, N Vuilleumier.
J Intern Med, 2012 Feb 15; 272(4). PMID: 22329401
Fucoidan, a sulfated polysaccharide from brown algae, against myocardial ischemia-reperfusion injury in rats via regulating the inflammation response.
Chunmei Li, Yonglin Gao, +3 authors, Jingwei Tian.
Food Chem Toxicol, 2011 Jun 08; 49(9). PMID: 21645579
Rare Copy Number Variants Identify Novel Genes in Sporadic Total Anomalous Pulmonary Vein Connection.
Xin Shi, Liangping Cheng, +11 authors, Sun Chen.
Front Genet, 2018 Dec 12; 9. PMID: 30532766    Free PMC article.
Novel high-throughput myofibroblast assays identify agonists with therapeutic potential in pulmonary fibrosis that act via EP2 and EP4 receptors.
Patrick Sieber, Anny Schäfer, +7 authors, Urs Lüthi.
PLoS One, 2018 Nov 30; 13(11). PMID: 30485339    Free PMC article.
Pathophysiology of ischaemia-reperfusion injury.
D L Carden, D N Granger.
J Pathol, 2000 Feb 24; 190(3). PMID: 10685060
Highly Cited. Review.
Use of the electrocardiogram in acute myocardial infarction.
Peter J Zimetbaum, Mark E Josephson.
N Engl J Med, 2003 Mar 07; 348(10). PMID: 12621138
Implementing myocardial infarction systems of care in low/middle-income countries.
Bruno R Nascimento, Luisa C Caldeira Brant, +2 authors, Antonio Luiz P Ribeiro.
Heart, 2018 Oct 01; 105(1). PMID: 30269080
Systematic Review.
Plant-based foods containing cell wall polysaccharides rich in specific active monosaccharides protect against myocardial injury in rat myocardial infarction models.
Sun Ha Lim, Yaesil Kim, +4 authors, Jongwon Lee.
Sci Rep, 2016 Dec 09; 6. PMID: 27929093    Free PMC article.
Identification of Differentially Expressed Genes between Original Breast Cancer and Xenograft Using Machine Learning Algorithms.
Deling Wang, Jia-Rui Li, +3 authors, Yu-Dong Cai.
Genes (Basel), 2018 Mar 15; 9(3). PMID: 29534550    Free PMC article.
Analysis of Expression Pattern of snoRNAs in Different Cancer Types with Machine Learning Algorithms.
Xiaoyong Pan, Lei Chen, +5 authors, Yu-Dong Cai.
Int J Mol Sci, 2019 May 06; 20(9). PMID: 31052553    Free PMC article.
Highly Cited.
Classification of Widely and Rarely Expressed Genes with Recurrent Neural Network.
Lei Chen, XiaoYong Pan, +3 authors, Yu-Dong Cai.
Comput Struct Biotechnol J, 2019 Jan 01; 17. PMID: 30595815    Free PMC article.
Monte Carlo feature selection for supervised classification.
Michal Draminski, Alvaro Rada-Iglesias, +3 authors, Jan Komorowski.
Bioinformatics, 2007 Dec 01; 24(1). PMID: 18048398
Tissue differences revealed by gene expression profiles of various cell lines.
Lei Chen, Xiaoyong Pan, +3 authors, Yu-Dong Cai.
J Cell Biochem, 2018 Oct 29;. PMID: 30368905
Circulating microRNA: a novel potential biomarker for early diagnosis of acute myocardial infarction in humans.
Guo-Kun Wang, Jia-Qi Zhu, +5 authors, Qing Jing.
Eur Heart J, 2010 Feb 18; 31(6). PMID: 20159880
Highly Cited.
Prognostic value of growth-differentiation factor-15 in patients with non-ST-elevation acute coronary syndrome.
Kai C Wollert, Tibor Kempf, +11 authors, Lars Wallentin.
Circulation, 2007 Feb 07; 115(8). PMID: 17283261
Impact of diabetes on mortality after the first myocardial infarction. The FINMONICA Myocardial Infarction Register Study Group.
H Miettinen, S Lehto, +5 authors, J Tuomilehto.
Diabetes Care, 1998 Apr 16; 21(1). PMID: 9538972
Highly Cited.
Valproic acid reversed pathologic endothelial cell gene expression profile associated with ischemia-reperfusion injury in a swine hemorrhagic shock model.
Marlin Wayne Causey, Shashikumar Salgar, +2 authors, Jonathan D Stallings.
J Vasc Surg, 2011 Nov 22; 55(4). PMID: 22100532
Innate and acquired immunity in atherogenesis.
Christoph J Binder, Mi-Kyung Chang, +4 authors, Joseph L Witztum.
Nat Med, 2002 Nov 02; 8(11). PMID: 12411948
Highly Cited. Review.
The early detection of asthma based on blood gene expression.
Shao-Bin Wang, Tao Huang.
Mol Biol Rep, 2018 Nov 14; 46(1). PMID: 30421126
Primary Tumor Site Specificity is Preserved in Patient-Derived Tumor Xenograft Models.
Lei Chen, Xiaoyong Pan, +4 authors, Yu-Dong Cai.
Front Genet, 2019 Aug 29; 10. PMID: 31456818    Free PMC article.
Myocardial ischemia/reperfusion injury is mediated by leukocytic toll-like receptor-2 and reduced by systemic administration of a novel anti-toll-like receptor-2 antibody.
Fatih Arslan, Mirjam B Smeets, +8 authors, Dominique P V de Kleijn.
Circulation, 2009 Dec 23; 121(1). PMID: 20026776
Highly Cited.
Explaining the increase in coronary heart disease mortality in Beijing between 1984 and 1999.
Julia Critchley, Jing Liu, +2 authors, Simon Capewell.
Circulation, 2004 Sep 01; 110(10). PMID: 15337690
Fc receptor biology.
M Daëron.
Annu Rev Immunol, 1997 Jan 01; 15. PMID: 9143687
Highly Cited. Review.
Acute myocardial infarction.
Harvey D White, Derek P Chew.
Lancet, 2008 Aug 19; 372(9638). PMID: 18707987
Highly Cited. Review.
Elevated plasma levels of interleukin-1 receptor antagonist and interleukin-10 in patients with acute myocardial infarction.
M Shibata, S Endo, +9 authors, K Hiramori.
J Interferon Cytokine Res, 1997 Mar 01; 17(3). PMID: 9085939
Universal definition of myocardial infarction.
Kristian Thygesen, Joseph S Alpert, Harvey D White, Joint ESC/ACCF/AHA/WHF Task Force for the Redefinition of Myocardial Infarction.
J Am Coll Cardiol, 2007 Nov 27; 50(22). PMID: 18036459
Highly Cited.
Identification of leukemia stem cell expression signatures through Monte Carlo feature selection strategy and support vector machine.
JiaRui Li, Lin Lu, +7 authors, Yu-Dong Cai.
Cancer Gene Ther, 2019 May 30; 27(1-2). PMID: 31138902
Activated toll-like receptor 4 in monocytes is associated with heart failure after acute myocardial infarction.
Mamoru Satoh, Yudai Shimoda, +5 authors, Motoyuki Nakamura.
Int J Cardiol, 2005 Jul 30; 109(2). PMID: 16051384
Momordica charantia polysaccharides ameliorate oxidative stress, hyperlipidemia, inflammation, and apoptosis during myocardial infarction by inhibiting the NF-κB signaling pathway.
Mohammad Raish.
Int J Biol Macromol, 2017 Jan 23; 97. PMID: 28109806
Downregulation of DLGAP1-Antisense RNA 1 Alleviates Vascular Endothelial Cell Injury Via Activation of the Phosphoinositide 3-kinase/Akt Pathway Results from an Acute Limb Ischemia Rat Model.
Guang-Hui Shen, Ye Song, +11 authors, Hai-Yang Wang.
Eur J Vasc Endovasc Surg, 2019 Nov 21; 59(1). PMID: 31744785
New Computational Tool Based on Machine-learning Algorithms for the Identification of Rhinovirus Infection-Related Genes.
Yan Xu, Yu-Hang Zhang, +3 authors, Yu-Dong Cai.
Comb Chem High Throughput Screen, 2019 Nov 30; 22(10). PMID: 31782358
Targeting Interleukin-1β Reduces Leukocyte Production After Acute Myocardial Infarction.
Hendrik B Sager, Timo Heidt, +11 authors, Matthias Nahrendorf.
Circulation, 2015 Sep 12; 132(20). PMID: 26358260    Free PMC article.
Highly Cited.
Predicting and analyzing early wake-up associated gene expressions by integrating GWAS and eQTL studies.
JiaRui Li, Tao Huang.
Biochim Biophys Acta Mol Basis Dis, 2017 Nov 08; 1864(6 Pt B). PMID: 29109033
Identifying key genes associated with acute myocardial infarction.
Ming Cheng, Shoukuan An, Junquan Li.
Medicine (Baltimore), 2017 Oct 20; 96(42). PMID: 29049183    Free PMC article.
Intermittent and recurrent hepatomegaly due to glycogen storage in a patient with type 1 diabetes: genetic analysis of the liver glycogen phosphorylase gene (PYGL).
Masako Tomihira, Eiji Kawasaki, +6 authors, Kiyohide Nunoi.
Diabetes Res Clin Pract, 2004 Jun 30; 65(2). PMID: 15223230
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, +9 authors, Christian von Mering.
Nucleic Acids Res, 2018 Nov 27; 47(D1). PMID: 30476243    Free PMC article.
Highly Cited.
Diabetes, 1965 Feb 01; 14. PMID: 14256056
Asp92Asn polymorphism in the myeloid IgA Fc receptor is associated with myocardial infarction in two disparate populations: CARE and WOSCOPS.
Olga A Iakoubova, Carmen H Tong, +18 authors, Frank M Sacks.
Arterioscler Thromb Vasc Biol, 2006 Sep 30; 26(12). PMID: 17008591
Expression and regulation of ST2, an interleukin-1 receptor family member, in cardiomyocytes and myocardial infarction.
Ellen O Weinberg, Masahisa Shimpo, +5 authors, Richard T Lee.
Circulation, 2002 Dec 04; 106(23). PMID: 12460879    Free PMC article.
Highly Cited.
Early matrix metalloproteinase-12 inhibition worsens post-myocardial infarction cardiac dysfunction by delaying inflammation resolution.
Rugmani Padmanabhan Iyer, Nicolle L Patterson, +4 authors, Merry L Lindsey.
Int J Cardiol, 2015 Mar 24; 185. PMID: 25797678    Free PMC article.
Failure of blood-island formation and vasculogenesis in Flk-1-deficient mice.
F Shalaby, J Rossant, +4 authors, A C Schuh.
Nature, 1995 Jul 06; 376(6535). PMID: 7596435
Highly Cited.
Prediction of Nitrated Tyrosine Residues in Protein Sequences by Extreme Learning Machine and Feature Selection Methods.
Lei Chen, ShaoPeng Wang, +4 authors, Yu-Dong Cai.
Comb Chem High Throughput Screen, 2018 Jun 01; 21(6). PMID: 29848272
Identifying Patients with Atrioventricular Septal Defect in Down Syndrome Populations by Using Self-Normalizing Neural Networks and Feature Selection.
Xiaoyong Pan, Xiaohua Hu, +5 authors, Yu Dong Cai.
Genes (Basel), 2018 Apr 13; 9(4). PMID: 29649131    Free PMC article.
Biomarkers identification for acute myocardial infarction detection via weighted gene co-expression network analysis.
Shu Zhang, Weixia Liu, +2 authors, Chunmei Deng.
Medicine (Baltimore), 2018 Feb 01; 96(47). PMID: 29381915    Free PMC article.
Identification of gene expression signatures across different types of neural stem cells with the Monte-Carlo feature selection method.
Lei Chen, JiaRui Li, +6 authors, Yu-Dong Cai.
J Cell Biochem, 2017 Nov 14; 119(4). PMID: 29130544
Next-generation sequencing identifies novel genes with rare variants in total anomalous pulmonary venous connection.
Xin Shi, Tao Huang, +8 authors, Yu Yu.
EBioMedicine, 2018 Nov 19; 38. PMID: 30448225    Free PMC article.
Identification of the copy number variant biomarkers for breast cancer subtypes.
Xiaoyong Pan, XiaoHua Hu, +5 authors, Yu-Dong Cai.
Mol Genet Genomics, 2018 Sep 12; 294(1). PMID: 30203254
Fcgamma receptor IIIA polymorphism as a risk-factor for coronary artery disease.
Sonia Gavasso, Ottar Nygård, +4 authors, Christian A Vedeler.
Atherosclerosis, 2005 May 25; 180(2). PMID: 15910853
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
B M Bolstad, R A Irizarry, M Astrand, T P Speed.
Bioinformatics, 2003 Jan 23; 19(2). PMID: 12538238
Highly Cited.
Heterozygous disruption of Flk-1 receptor leads to myocardial ischaemia reperfusion injury in mice: application of affymetrix gene chip analysis.
M Thirunavukkarasu, S Addya, +6 authors, N Maulik.
J Cell Mol Med, 2008 Feb 13; 12(4). PMID: 18266966    Free PMC article.
Myocardial Infarction: Symptoms and Treatments.
Lei Lu, Min Liu, +2 authors, Peiying Zhang.
Cell Biochem Biophys, 2015 Feb 02; 72(3). PMID: 25638347
Third universal definition of myocardial infarction.
Kristian Thygesen, Joseph S Alpert, +116 authors, Daniel R Wagner.
J Am Coll Cardiol, 2012 Sep 11; 60(16). PMID: 22958960
Highly Cited.
Glycogen phosphorylase isoenzyme BB in diagnosis of myocardial ischaemic injury and infarction.
E G Krause, G Rabitzsch, +2 authors, B Puschendorf.
Mol Cell Biochem, 1996 Jul 01; 160-161. PMID: 8901485
Association of the Trp719Arg polymorphism in kinesin-like protein 6 with myocardial infarction and coronary heart disease in 2 prospective trials: the CARE and WOSCOPS trials.
Olga A Iakoubova, Carmen H Tong, +13 authors, Frank M Sacks.
J Am Coll Cardiol, 2008 Jan 29; 51(4). PMID: 18222353
Impaired insulin signaling accelerates cardiac mitochondrial dysfunction after myocardial infarction.
Sandra Sena, Ping Hu, +6 authors, Sheldon E Litwin.
J Mol Cell Cardiol, 2009 Mar 03; 46(6). PMID: 19249310    Free PMC article.
It's time for a change to a troponin standard.
A S Jaffe, J Ravkilde, +4 authors, H Katus.
Circulation, 2000 Sep 12; 102(11). PMID: 10982533
Discriminating cirRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm with feature selection.
Lei Chen, Yu-Hang Zhang, +4 authors, Yu-Dong Cai.
Mol Genet Genomics, 2017 Sep 16; 293(1). PMID: 28913654
Circulating interleukin-1 beta, interleukin-6, tumor necrosis factor-alpha, and soluble ICAM-1 in patients with chronic stable angina and myocardial infarction.
Y Balbay, H Tikiz, +3 authors, S Korkmaz.
Angiology, 2001 Mar 03; 52(2). PMID: 11228083
National Academy of Clinical Biochemistry Laboratory Medicine Practice Guidelines: clinical characteristics and utilization of biochemical markers in acute coronary syndromes.
David A Morrow, Christopher P Cannon, +9 authors, National Academy of Clinical Biochemistry.
Clin Chem, 2007 Mar 27; 53(4). PMID: 17384001
TLR2 and TLR4 in ischemia reperfusion injury.
F Arslan, B Keogh, P McGuirk, A E Parker.
Mediators Inflamm, 2010 Jul 16; 2010. PMID: 20628516    Free PMC article.
Trends in presenting characteristics and hospital mortality among patients with ST elevation and non-ST elevation myocardial infarction in the National Registry of Myocardial Infarction from 1990 to 2006.
William J Rogers, Paul D Frederick, +8 authors, William J French.
Am Heart J, 2008 Nov 27; 156(6). PMID: 19032996
The prognostic value of B-type natriuretic peptide in patients with acute coronary syndromes.
J A de Lemos, D A Morrow, +6 authors, E Braunwald.
N Engl J Med, 2001 Oct 06; 345(14). PMID: 11586953
Highly Cited.
Cross talk of chromosome instability, CpG island methylator phenotype and mismatch repair in colorectal cancer.
Tian-Ming Zhang, Tao Huang, Rong-Fei Wang.
Oncol Lett, 2018 Jul 17; 16(2). PMID: 30008861    Free PMC article.
Screening for Core Genes Related to Pathogenesis of Alzheimer's Disease.
Longxiu Yang, Yuan Qin, Chongdong Jian.
Front Cell Dev Biol, 2021 May 11; 9. PMID: 33968940    Free PMC article.