{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,11,16]],"date-time":"2023-11-16T00:47:27Z","timestamp":1700095647848},"reference-count":80,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2023,11,15]],"date-time":"2023-11-15T00:00:00Z","timestamp":1700006400000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Science, Research and Innovation Fund"},{"DOI":"10.13039\/501100004705","name":"King Mongkut\u2019s University of Technology","doi-asserted-by":"crossref","award":["KMUTNB-FF-66-08"],"id":[{"id":"10.13039\/501100004705","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"\nBackground<\/jats:title>\nIdentifying the genes responsible for diseases requires precise prioritization of significant genes. Gene expression analysis enables differentiation between gene expressions in disease and normal samples. Increasing the number of high-quality samples enhances the strength of evidence regarding gene involvement in diseases. This process has led to the discovery of disease biomarkers through the collection of diverse gene expression data.<\/jats:p>\n<\/jats:sec>\n\nMethods<\/jats:title>\nThis study presents GeneCompete, a web-based tool that integrates gene expression data from multiple platforms and experiments to identify the most promising biomarkers. GeneCompete incorporates a novel union strategy and eight well-established ranking methods, including Win-Loss, Massey, Colley, Keener, Elo, Markov, PageRank, and Bi-directional PageRank algorithms, to prioritize genes across multiple gene expression datasets. Each gene in the competition is assigned a score based on log-fold change values, and significant genes are determined as winners.<\/jats:p>\n<\/jats:sec>\n\nResults<\/jats:title>\nWe tested the tool on the expression datasets of Hypertrophic cardiomyopathy (HCM) and the datasets from Microarray Quality Control (MAQC) project, which include both microarray and RNA-Sequencing techniques. The results demonstrate that all ranking scores have more power to predict new occurrence datasets than the classical method. Moreover, the PageRank method with a union strategy delivers the best performance for both up-regulated and down-regulated genes. Furthermore, the top-ranking genes exhibit a strong association with the disease. For MAQC, the two-sides ranking score shows a high relationship with TaqMan validation set in all log-fold change thresholds.<\/jats:p>\n<\/jats:sec>\n\nConclusion<\/jats:title>\nGeneCompete is a powerful web-based tool that revolutionizes the identification of disease-causing genes through the integration of gene expression data from multiple platforms and experiments.<\/jats:p>\n<\/jats:sec>","DOI":"10.7717\/peerj-cs.1686","type":"journal-article","created":{"date-parts":[[2023,11,15]],"date-time":"2023-11-15T08:38:45Z","timestamp":1700037525000},"page":"e1686","source":"Crossref","is-referenced-by-count":0,"title":["GeneCompete: an integrative tool of a novel union algorithm with various ranking techniques for multiple gene expression data"],"prefix":"10.7717","volume":"9","author":[{"given":"Panisa","family":"Janyasupab","sequence":"first","affiliation":[{"name":"Department of Mathematics and Computer Science\/Faculty of Science, Chulalongkorn University, Bangkok, Thailand"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-3439-6619","authenticated-orcid":true,"given":"Apichat","family":"Suratanee","sequence":"additional","affiliation":[{"name":"Department of Mathematics\/Faculty of Applied Science, King Mongkut\u2019s University of Technology North Bangkok, Bangkok, Thailand"},{"name":"Intelligent and Nonlinear Dynamics Innovations Research Center, Science and Technology Research Institute, King Mongkut\u2019s University of Technology North Bangkok, Bangkok, Thailand"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-0416-8316","authenticated-orcid":true,"given":"Kitiporn","family":"Plaimas","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science\/Faculty of Science, Chulalongkorn University, Bangkok, Thailand"},{"name":"Omics Science and Bioinformatics Center\/Faculty of Science, Chulalongkorn University, Bangkok, Thailand"}]}],"member":"4443","published-online":{"date-parts":[[2023,11,15]]},"reference":[{"key":"10.7717\/peerj-cs.1686\/ref-1","doi-asserted-by":"publisher","first-page":"3472","DOI":"10.3390\/ijms21103472","article-title":"Identification of upstream transcriptional regulators of ischemic cardiomyopathy using cardiac RNA-seq meta-analysis","volume":"21","author":"Alimadadi","year":"2020","journal-title":"International Journal of Molecular Sciences"},{"key":"10.7717\/peerj-cs.1686\/ref-2","article-title":"Genetic polymorphisms that playing role in development of hypertrophic cardiomyopathy","volume-title":"Practical Applications of Electrocardiogram","author":"Alkanli","year":"2019"},{"key":"10.7717\/peerj-cs.1686\/ref-3","doi-asserted-by":"publisher","first-page":"e0201422","DOI":"10.1371\/journal.pone.0201422","article-title":"The extracellular matrix proteoglycan fibromodulin is upregulated in clinical and experimental heart failure and affects cardiac remodeling","volume":"13","author":"Anden\u00e6s","year":"2018","journal-title":"PLoS ONE"},{"key":"10.7717\/peerj-cs.1686\/ref-4","doi-asserted-by":"publisher","first-page":"e0232271","DOI":"10.1371\/journal.pone.0232271","article-title":"Benchmarking RNA-seq differential expression analysis methods using spike-in and simulation data","volume":"15","author":"Baik","year":"2020","journal-title":"PLoS ONE"},{"key":"10.7717\/peerj-cs.1686\/ref-5","doi-asserted-by":"publisher","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets\u2014Update","volume":"41","author":"Barrett","year":"2012","journal-title":"Nucleic acids research"},{"key":"10.7717\/peerj-cs.1686\/ref-6","doi-asserted-by":"publisher","first-page":"2318","DOI":"10.3390\/biomedicines10092318","article-title":"Transcriptomic harmonization as the way for suppressing cross-platform bias and batch effect","volume":"10","author":"Borisov","year":"2022","journal-title":"Biomedicines"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-7","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.jacbts.2020.11.008","article-title":"Proteomic architecture of valvular extracellular matrix: FNDC1 and MXRA5 are new biomarkers of aortic stenosis","volume":"6","author":"Bouchareb","year":"2021","journal-title":"Basic to Translational Science"},{"issue":"16","key":"10.7717\/peerj-cs.1686\/ref-8","doi-asserted-by":"publisher","first-page":"e015342","DOI":"10.1161\/JAHA.119.015342","article-title":"Right ventricle has normal myofilament function but shows perturbations in the expression of extracellular matrix genes in patients with tetralogy of fallot undergoing pulmonary valve replacement","volume":"9","author":"Brayson","year":"2020","journal-title":"Journal of the American Heart Association"},{"issue":"1\u20137","key":"10.7717\/peerj-cs.1686\/ref-9","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/S0169-7552(98)00110-X","article-title":"The anatomy of a large-scale hypertextual web search engine","volume":"30","author":"Brin","year":"1998","journal-title":"Computer Networks and ISDN Systems"},{"key":"10.7717\/peerj-cs.1686\/ref-10","doi-asserted-by":"publisher","first-page":"946229","DOI":"10.3389\/fcvm.2022.946229","article-title":"Identification of key genes for hypertrophic cardiomyopathy using integrated network analysis of differential lncRNA and gene expression","volume":"9","author":"Cao","year":"2022","journal-title":"Frontiers in Cardiovascular Medicine"},{"issue":"7921","key":"10.7717\/peerj-cs.1686\/ref-11","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1038\/s41586-022-04817-8","article-title":"Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy","volume":"608","author":"Chaffin","year":"2022","journal-title":"Nature"},{"issue":"8","key":"10.7717\/peerj-cs.1686\/ref-12","doi-asserted-by":"publisher","first-page":"1225","DOI":"10.1038\/s41591-018-0046-2","article-title":"Suppression of detyrosinated microtubules improves cardiomyocyte function in human heart failure","volume":"24","author":"Chen","year":"2018","journal-title":"Nature Medicine"},{"issue":"5","key":"10.7717\/peerj-cs.1686\/ref-13","doi-asserted-by":"publisher","first-page":"H1687","DOI":"10.1152\/ajpheart.00399.2010","article-title":"Protease corin expression and activity in failing hearts","volume":"299","author":"Chen","year":"2010","journal-title":"American Journal of Physiology-Heart and Circulatory Physiology"},{"issue":"10","key":"10.7717\/peerj-cs.1686\/ref-14","doi-asserted-by":"publisher","first-page":"1419","DOI":"10.3390\/biom12101419","article-title":"Systemic biomarkers and unique pathways in different phenotypes of heart failure with preserved ejection fraction","volume":"12","author":"Chen","year":"2022","journal-title":"Biomolecules"},{"key":"10.7717\/peerj-cs.1686\/ref-15","doi-asserted-by":"publisher","first-page":"e001974","DOI":"10.1161\/CIRCGEN.117.001974","article-title":"Proteomic analysis of the myocardium in hypertrophic obstructive cardiomyopathy","volume":"11","author":"Coats","year":"2018","journal-title":"Circulation: Genomic and Precision Medicine"},{"key":"10.7717\/peerj-cs.1686\/ref-16","volume-title":"Colley\u2019s bias free college football ranking method","author":"Colley","year":"2002"},{"issue":"10","key":"10.7717\/peerj-cs.1686\/ref-17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2022\/8680178","article-title":"Dysfunctional network and mutation genes of hypertrophic cardiomyopathy","volume":"2022","author":"Cui","year":"2022","journal-title":"Journal of Healthcare Engineering"},{"issue":"3","key":"10.7717\/peerj-cs.1686\/ref-18","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1515\/jqas-2017-0098","article-title":"A network diffusion ranking family that includes the methods of Markov, Massey, and Colley","volume":"14","author":"Devlin","year":"2018","journal-title":"Journal of Quantitative Analysis in Sports"},{"issue":"3","key":"10.7717\/peerj-cs.1686\/ref-19","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1093\/bioinformatics\/btz652","article-title":"Gene relevance based on multiple evidences in complex networks","volume":"36","author":"Di Nanni","year":"2020","journal-title":"Bioinformatics"},{"key":"10.7717\/peerj-cs.1686\/ref-20","volume-title":"The rating of chessplayers, past and present","author":"Elo","year":"1978"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-21","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1186\/s12872-022-02759-7","article-title":"Exploration of dilated cardiomyopathy for biomarkers and immune microenvironment: evidence from RNA-seq","volume":"22","author":"Fang","year":"2022","journal-title":"BMC Cardiovascular Disorders"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-22","doi-asserted-by":"publisher","first-page":"2551","DOI":"10.1038\/s41467-020-16345-y","article-title":"FoxO1-Dio2 signaling axis governs cardiomyocyte thyroid hormone metabolism and hypertrophic growth","volume":"11","author":"Ferdous","year":"2020","journal-title":"Nature Communications"},{"issue":"7","key":"10.7717\/peerj-cs.1686\/ref-23","doi-asserted-by":"publisher","first-page":"2119","DOI":"10.1109\/JBHI.2019.2953978","article-title":"Towards improving skin cancer diagnosis by integrating microarray and RNA-seq datasets","volume":"24","author":"G\u00e1lvez","year":"2019","journal-title":"IEEE Journal of Biomedical and Health Informatics"},{"issue":"7","key":"10.7717\/peerj-cs.1686\/ref-24","doi-asserted-by":"crossref","first-page":"617","DOI":"10.5152\/akd.2014.4972","article-title":"Association between non-coding polymorphisms of HOPX gene and syncope in hypertrophic cardiomyopathy","volume":"14","author":"G\u00fcle\u00e7","year":"2014","journal-title":"Anadolu Kardiyoloji Dergisi"},{"key":"10.7717\/peerj-cs.1686\/ref-25","doi-asserted-by":"publisher","first-page":"1248","DOI":"10.3389\/fcell.2022.894635","article-title":"Myosin heavy chain converter domain mutations drive early-stage changes in extracellular matrix dynamics in hypertrophic cardiomyopathy","author":"Hsieh","year":"2022","journal-title":"Frontiers in Cell and Developmental Biology"},{"key":"10.7717\/peerj-cs.1686\/ref-26","first-page":"325","article-title":"Heterogeneous data analysis of hypertrophic cardiomyopathy to prioritize important genes","author":"Janyasupab","year":"2022"},{"key":"10.7717\/peerj-cs.1686\/ref-27","doi-asserted-by":"publisher","article-title":"Identification of key modules and hub genes in hypertrophic cardiomyopathy based on integrative weighted gene co-expression network analysis","author":"Jiang","year":"2021","DOI":"10.21203\/rs.3.rs-915958\/v1"},{"issue":"4","key":"10.7717\/peerj-cs.1686\/ref-28","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.21037\/jtd-22-22","article-title":"Integrated gene expression profiling analysis reveals SERPINA3, FCN3, FREM1, MNS1 as candidate biomarkers in heart failure and their correlation with immune infiltration","volume":"14","author":"Jiang","year":"2022","journal-title":"Journal of Thoracic Disease"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-29","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1137\/1035004","article-title":"The perron-frobenius theorem and the ranking of football teams","volume":"35","author":"Keener","year":"1993","journal-title":"SIAM Review"},{"issue":"4","key":"10.7717\/peerj-cs.1686\/ref-30","doi-asserted-by":"publisher","first-page":"655","DOI":"10.3390\/genes13040655","article-title":"Identification of potential key genes in prostate cancer with gene expression, pivotal pathways and regulatory networks analysis using integrated bioinformatics methods","volume":"13","author":"Khan","year":"2022","journal-title":"Genes"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12872-021-02146-8","article-title":"Identification of candidate biomarkers and therapeutic agents for heart failure by bioinformatics analysis","volume":"21","author":"Kolur","year":"2021","journal-title":"BMC Cardiovascular Disorders"},{"key":"10.7717\/peerj-cs.1686\/ref-32","doi-asserted-by":"crossref","volume-title":"Who\u2019s# 1?: the science of rating and ranking","author":"Langville","year":"2012","DOI":"10.1515\/9781400841677"},{"issue":"Suppl_3","key":"10.7717\/peerj-cs.1686\/ref-33","doi-asserted-by":"publisher","first-page":"A17402","DOI":"10.1161\/circ.142.suppl_3.17402","article-title":"Single nuclei RNA-sequencing of human hypertrophic cardiomyopathy myectomy samples reveals common novel mechanisms of pathogenesis and potential therapeutic targets regardless of genotype","volume":"142","author":"Larson","year":"2020","journal-title":"Circulation"},{"issue":"9","key":"10.7717\/peerj-cs.1686\/ref-34","doi-asserted-by":"publisher","first-page":"888","DOI":"10.1038\/nbt.3000","article-title":"Detecting and correcting systematic variation in large-scale RNA sequencing data","volume":"32","author":"Li","year":"2014","journal-title":"Nature Biotechnology"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-35","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41597-019-0094-6","article-title":"Long non-coding and coding RNA profiling using strand-specific RNA-seq in human hypertrophic cardiomyopathy","volume":"6","author":"Liu","year":"2019","journal-title":"Scientific Data"},{"issue":"12","key":"10.7717\/peerj-cs.1686\/ref-36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biology"},{"key":"10.7717\/peerj-cs.1686\/ref-37","doi-asserted-by":"publisher","first-page":"1854","DOI":"10.3389\/fcvm.2021.747803","article-title":"Robust rank aggregation and least absolute shrinkage and selection operator analysis of novel gene signatures in dilated cardiomyopathy","author":"Ma","year":"2021a","journal-title":"Frontiers in Cardiovascular Medicine"},{"key":"10.7717\/peerj-cs.1686\/ref-38","doi-asserted-by":"publisher","first-page":"823","DOI":"10.2147\/PGPM.S314880","article-title":"Identification of underlying hub genes associated with hypertrophic cardiomyopathy by integrated bioinformatics analysis","author":"Ma","year":"2021b","journal-title":"Pharmacogenomics and Personalized Medicine"},{"issue":"9","key":"10.7717\/peerj-cs.1686\/ref-39","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1038\/nbt1239","article-title":"The microarray quality control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements","volume":"24","author":"MAQC Consortium","year":"2006","journal-title":"Nature Biotechnology"},{"issue":"9","key":"10.7717\/peerj-cs.1686\/ref-40","doi-asserted-by":"publisher","first-page":"903","DOI":"10.1038\/nbt.2957","article-title":"A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the sequencing quality control consortium","volume":"32","author":"MAQC Consortium","year":"2014","journal-title":"Nature Biotechnology"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-41","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1038\/s41467-021-21146-y","article-title":"Individualized interactomes for network-based precision medicine in hypertrophic cardiomyopathy with implications for other clinical pathophenotypes","volume":"12","author":"Maron","year":"2021","journal-title":"Nature Communications"},{"key":"10.7717\/peerj-cs.1686\/ref-42","first-page":"1077","volume-title":"Statistical models applied to the rating of sports teams","author":"Massey","year":"1997"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-43","doi-asserted-by":"publisher","first-page":"5125","DOI":"10.1038\/ncomms6125","article-title":"Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures","volume":"5","author":"Munro","year":"2014","journal-title":"Nature Communications"},{"key":"10.7717\/peerj-cs.1686\/ref-44","doi-asserted-by":"publisher","first-page":"663787","DOI":"10.3389\/fgene.2021.663787","article-title":"Integrated analysis of microarray and RNA-Seq data for the identification of hub genes and networks involved in the pancreatic cancer","volume":"12","author":"Nisar","year":"2021","journal-title":"Frontiers in Genetics"},{"issue":"5","key":"10.7717\/peerj-cs.1686\/ref-45","doi-asserted-by":"publisher","first-page":"232","DOI":"10.3390\/info13050232","article-title":"A forward-looking approach to compare ranking methods for sports","volume":"13","author":"Ochieng","year":"2022","journal-title":"Information"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-46","doi-asserted-by":"publisher","first-page":"3027","DOI":"10.1038\/s41467-022-30682-0","article-title":"Mapping the cardiac vascular niche in heart failure","volume":"13","author":"Peisker","year":"2022","journal-title":"Nature Communications"},{"key":"10.7717\/peerj-cs.1686\/ref-47","article-title":"Computer to AID in basketball championship selection","volume":"4","author":"Pickle","year":"1981","journal-title":"NCAA News"},{"issue":"7","key":"10.7717\/peerj-cs.1686\/ref-48","doi-asserted-by":"publisher","first-page":"e019667","DOI":"10.1161\/JAHA.120.019667","article-title":"Consensus transcriptional landscape of human end-stage heart failure","volume":"10","author":"Ramirez Flores","year":"2021","journal-title":"Journal of the American Heart Association"},{"issue":"21","key":"10.7717\/peerj-cs.1686\/ref-49","doi-asserted-by":"publisher","first-page":"1714","DOI":"10.1161\/CIRCULATIONAHA.121.053575","article-title":"Altered cardiac energetics and mitochondrial dysfunction in hypertrophic cardiomyopathy","volume":"144","author":"Ranjbarvaziri","year":"2021","journal-title":"Circulation"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-50","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12872-018-0867-4","article-title":"Whole-exome sequencing identifies R1279X of MYH6 gene to be associated with congenital heart disease","volume":"18","author":"Razmara","year":"2018","journal-title":"BMC Cardiovascular Disorders"},{"issue":"6","key":"10.7717\/peerj-cs.1686\/ref-51","doi-asserted-by":"publisher","first-page":"5573","DOI":"10.3892\/mmr.2016.5931","article-title":"RNA\u2010seq profiling of mRNA associated with hypertrophic cardiomyopathy","volume":"14","author":"Ren","year":"2016","journal-title":"Molecular Medicine Reports"},{"issue":"7","key":"10.7717\/peerj-cs.1686\/ref-52","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"Limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-53","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"issue":"25","key":"10.7717\/peerj-cs.1686\/ref-54","doi-asserted-by":"publisher","first-page":"41432","DOI":"10.18632\/oncotarget.18186","article-title":"Identification of molecular biomarkers for pancreatic cancer with mRMR shortest path method","volume":"8","author":"Shen","year":"2017","journal-title":"Oncotarget"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-55","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1038\/s41392-022-01055-2","article-title":"Epigenetic regulation in cardiovascular disease: mechanisms and advances in clinical trials","volume":"7","author":"Shi","year":"2022","journal-title":"Signal Transduction and Targeted Therapy"},{"key":"10.7717\/peerj-cs.1686\/ref-56","doi-asserted-by":"crossref","DOI":"10.1007\/0-387-29362-0_23","article-title":"LIMMA: linear models for microarray data","volume-title":"Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Statistics for Biology and Health","author":"Smyth","year":"2005"},{"issue":"12","key":"10.7717\/peerj-cs.1686\/ref-57","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-014-0523-y","article-title":"An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era","volume":"15","author":"Su","year":"2014","journal-title":"Genome Biology"},{"issue":"12","key":"10.7717\/peerj-cs.1686\/ref-58","doi-asserted-by":"publisher","first-page":"12554","DOI":"10.21037\/apm-21-3561","article-title":"Carbonic anhydrase 2 and 3 as risk biomarkers for dilated cardiomyopathy associated heart failure","volume":"10","author":"Su","year":"2021","journal-title":"Annals of Palliative Medicine"},{"issue":"17","key":"10.7717\/peerj-cs.1686\/ref-59","doi-asserted-by":"publisher","first-page":"e99","DOI":"10.1093\/nar\/gkab554","article-title":"Rank-in: enabling integrative analysis across microarray and RNA-seq for cancer","volume":"49","author":"Tang","year":"2021","journal-title":"Nucleic Acids Research"},{"issue":"23","key":"10.7717\/peerj-cs.1686\/ref-60","doi-asserted-by":"publisher","first-page":"6098","DOI":"10.3390\/ijms20236098","article-title":"RankerGUI: a computational framework to compare differential gene expression profiles using rank based statistics","volume":"20","author":"Thind","year":"2019","journal-title":"International Journal of Molecular Sciences"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-61","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-018-20114-9","article-title":"Genetic basis of cardiomyopathy and the genotypes involved in prognosis and left ventricular reverse remodeling","volume":"8","author":"Tobita","year":"2018","journal-title":"Scientific Reports"},{"issue":"6","key":"10.7717\/peerj-cs.1686\/ref-62","doi-asserted-by":"publisher","first-page":"1056","DOI":"10.1016\/j.yjmcc.2011.02.015","article-title":"Homeodomain only protein x is down-regulated in human heart failure","volume":"50","author":"Trivedi","year":"2011","journal-title":"Journal of Molecular and Cellular Cardiology"},{"key":"10.7717\/peerj-cs.1686\/ref-63","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1016\/j.yjmcc.2013.05.019","article-title":"CCN2 plays a key role in extracellular matrix gene expression in severe hypertrophic cardiomyopathy and heart failure","volume":"62","author":"Tsoutsman","year":"2013","journal-title":"Journal of Molecular and Cellular Cardiology"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-64","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1504\/IJOR.2018.091200","article-title":"A proposed voting scheme to reduce the sensitivity of the Markov method","volume":"32","author":"Vaziri","year":"2018","journal-title":"International Journal of Operational Research"},{"key":"10.7717\/peerj-cs.1686\/ref-65","first-page":"155","article-title":"The five greatest applications of Markov chains","author":"Von Hilgers","year":"2006"},{"issue":"9","key":"10.7717\/peerj-cs.1686\/ref-66","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1038\/nbt.3001","article-title":"The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance","volume":"32","author":"Wang","year":"2014","journal-title":"Nature Biotechnology"},{"issue":"4","key":"10.7717\/peerj-cs.1686\/ref-67","doi-asserted-by":"publisher","first-page":"636","DOI":"10.1093\/cvr\/cvq133","article-title":"Up-regulation of type 2 iodothyronine deiodinase in dilated cardiomyopathy","volume":"87","author":"Wang","year":"2010","journal-title":"Cardiovascular Research"},{"key":"10.7717\/peerj-cs.1686\/ref-68","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-11-S6-S10","article-title":"Evaluation of gene expression data generated from expired Affymetrix GeneChip\u00ae microarrays using MAQC reference RNA samples","author":"Wen","year":"2010","journal-title":"BMC bioinformatics: BioMed Central"},{"issue":"11","key":"10.7717\/peerj-cs.1686\/ref-69","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.2217\/bmm.15.96","article-title":"NETBAGs: a network-based clustering approach with gene signatures for cancer subtyping analysis","volume":"9","author":"Wu","year":"2015","journal-title":"Biomarkers in Medicine"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-70","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12872-021-02147-7","article-title":"Integration of transcriptomic data identifies key hallmark genes in hypertrophic cardiomyopathy","volume":"21","author":"Xu","year":"2021","journal-title":"BMC Cardiovascular Disorders"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-71","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12872-015-0056-7","article-title":"Microarray profiling of long non-coding RNA (lncRNA) associated with hypertrophic cardiomyopathy","volume":"15","author":"Yang","year":"2015","journal-title":"BMC Cardiovascular Disorders"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-72","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.jphs.2019.04.003","article-title":"Knockdown of Sfrp4 attenuates apoptosis to protect against myocardial ischemia\/reperfusion injury","volume":"140","author":"Zeng","year":"2019","journal-title":"Journal of Pharmacological Sciences"},{"key":"10.7717\/peerj-cs.1686\/ref-73","doi-asserted-by":"publisher","first-page":"250","DOI":"10.3389\/fimmu.2022.975367","article-title":"Role of the CCL2-CCR2 axis in cardiovascular disease: pathogenesis and clinical implications","volume":"13","author":"Zhang","year":"2022","journal-title":"Frontiers in Immunology"},{"key":"10.7717\/peerj-cs.1686\/ref-74","doi-asserted-by":"publisher","first-page":"696321","DOI":"10.3389\/fcvm.2021.696321","article-title":"Bioinformatics and immune infiltration analyses reveal the key pathway and immune cells in the pathogenesis of hypertrophic cardiomyopathy","volume":"8","author":"Zhang","year":"2021","journal-title":"Frontiers in Cardiovascular Medicine"},{"issue":"12","key":"10.7717\/peerj-cs.1686\/ref-75","doi-asserted-by":"publisher","first-page":"1918","DOI":"10.1161\/CIRCRESAHA.116.308688","article-title":"Deletion of interleukin-6 attenuates pressure overload-induced left ventricular hypertrophy and dysfunction","volume":"118","author":"Zhao","year":"2016","journal-title":"Circulation Research"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-76","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12929-018-0459-8","article-title":"Identification of target genes in cardiomyopathy with fibrosis and cardiac remodeling","volume":"25","author":"Zhao","year":"2018","journal-title":"Journal of Biomedical Science"},{"key":"10.7717\/peerj-cs.1686\/ref-77","doi-asserted-by":"publisher","first-page":"80","DOI":"10.18632\/aging.204547","article-title":"Identification MNS1, SERP1NA3 and FCN3 as the potential immune-related key genes involved in ischaemic cardiomyopathy by random forest and nomogram","volume":"15","author":"Zheng","year":"2023","journal-title":"Sedentary Life and Nutrition"},{"issue":"25","key":"10.7717\/peerj-cs.1686\/ref-78","doi-asserted-by":"publisher","first-page":"119956","DOI":"10.1016\/j.lfs.2021.119956","article-title":"Identification and verification of promising diagnostic biomarkers in patients with hypertrophic cardiomyopathy associate with immune cell infiltration characteristics","volume":"285","author":"Zheng","year":"2021","journal-title":"Life Sciences"},{"issue":"3","key":"10.7717\/peerj-cs.1686\/ref-79","doi-asserted-by":"publisher","first-page":"108168","DOI":"10.1016\/j.knosys.2022.108168","article-title":"Improving PageRank using sports results modeling","volume":"241","author":"Zhou","year":"2022","journal-title":"Knowledge-Based Systems"},{"issue":"1","key":"10.7717\/peerj-cs.1686\/ref-80","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12920-020-00750-9","article-title":"Weighted correlation network bioinformatics uncovers a key molecular biosignature driving the left-sided heart failure","volume":"13","author":"Zhou","year":"2020","journal-title":"BMC Medical Genomics"}],"container-title":["PeerJ Computer Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/peerj.com\/articles\/cs-1686.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/cs-1686.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/cs-1686.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/cs-1686.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,15]],"date-time":"2023-11-15T08:39:14Z","timestamp":1700037554000},"score":1,"resource":{"primary":{"URL":"https:\/\/peerj.com\/articles\/cs-1686"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,15]]},"references-count":80,"alternative-id":["10.7717\/peerj-cs.1686"],"URL":"https:\/\/doi.org\/10.7717\/peerj-cs.1686","archive":["CLOCKSS","LOCKSS","Portico"],"relation":{},"ISSN":["2376-5992"],"issn-type":[{"value":"2376-5992","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,11,15]]},"article-number":"e1686"}}