{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T21:07:14Z","timestamp":1761599234437,"version":"3.37.3"},"reference-count":101,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2022,6,21]],"date-time":"2022-06-21T00:00:00Z","timestamp":1655769600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2022,6,21]],"date-time":"2022-06-21T00:00:00Z","timestamp":1655769600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Netw Model Anal Health Inform Bioinforma"],"published-print":{"date-parts":[[2022,12]]},"DOI":"10.1007\/s13721-022-00365-3","type":"journal-article","created":{"date-parts":[[2022,6,21]],"date-time":"2022-06-21T14:09:42Z","timestamp":1655820582000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["SGAClust: Semi-supervised Graph Attraction Clustering of gene expression data"],"prefix":"10.1007","volume":"11","author":[{"given":"Koyel","family":"Mandal","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rosy","family":"Sarmah","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,6,21]]},"reference":[{"issue":"1","key":"365_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-018-1536-8","volume":"19","author":"B Abu-Jamous","year":"2018","unstructured":"Abu-Jamous B, Kelly S (2018) Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data. Genome Biol 19(1):1\u201311","journal-title":"Genome Biol"},{"issue":"1","key":"365_CR2","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/ng765","volume":"30","author":"SA Armstrong","year":"2002","unstructured":"Armstrong SA, Staunton JE, Silverman LB, Pieters R, den Boer ML, Minden MD, Sallan SE, Lander ES, Golub TR, Korsmeyer SJ (2002) Mll translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet 30(1):41\u201347","journal-title":"Nat Genet"},{"key":"365_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.omto.2017.10.002","volume":"8","author":"D-H Bach","year":"2018","unstructured":"Bach D-H, Park HJ, Lee SK (2018) The dual role of bone morphogenetic proteins in cancer. Mol Therapy-Oncolytics 8:1\u201313","journal-title":"Mol Therapy-Oncolytics"},{"issue":"3\u20134","key":"365_CR4","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1089\/106652799318274","volume":"6","author":"A Ben-Dor","year":"1999","unstructured":"Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comput Biol 6(3\u20134):281\u2013297","journal-title":"J Comput Biol"},{"issue":"18","key":"365_CR5","doi-asserted-by":"publisher","first-page":"2502","DOI":"10.1093\/bioinformatics\/btg363","volume":"19","author":"GF Berriz","year":"2003","unstructured":"Berriz GF, King OD, Bryant B, Sander C, Roth FP (2003) Characterizing gene sets with funcassociate. Bioinformatics 19(18):2502\u20132504","journal-title":"Bioinformatics"},{"issue":"24","key":"365_CR6","doi-asserted-by":"publisher","first-page":"13790","DOI":"10.1073\/pnas.191502998","volume":"98","author":"A Bhattacharjee","year":"2001","unstructured":"Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M et al (2001) Classification of human lung carcinomas by mrna expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci 98(24):13790\u201313795","journal-title":"Proc Natl Acad Sci"},{"issue":"1","key":"365_CR7","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1016\/j.jmva.2004.02.011","volume":"90","author":"J Bryan","year":"2004","unstructured":"Bryan J (2004) Problems in gene clustering based on gene expression data. J Multivariate Anal 90(1):44\u201366","journal-title":"J Multivariate Anal"},{"issue":"1","key":"365_CR8","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1186\/1471-2164-11-274","volume":"11","author":"AH Chen","year":"2010","unstructured":"Chen AH, Tsau Y-W, Lin C-H (2010) Novel methods to identify biologically relevant genes for leukemia and prostate cancer from gene expression profiles. BMC genomics 11(1):274","journal-title":"BMC genomics"},{"issue":"31","key":"365_CR9","doi-asserted-by":"publisher","first-page":"51920","DOI":"10.18632\/oncotarget.17231","volume":"8","author":"N Coccaro","year":"2017","unstructured":"Coccaro N, Tota G, Zagaria A, Anelli L, Specchia G, Albano F (2017) Setbp1 dysregulation in congenital disorders and myeloid neoplasms. Oncotarget 8(31):51920","journal-title":"Oncotarget"},{"issue":"1","key":"365_CR10","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1186\/1471-2105-9-497","volume":"9","author":"MC de Souto","year":"2008","unstructured":"de Souto MC, Costa IG, de Araujo DS, Ludermir TB, Schliep A (2008) Clustering cancer gene expression data: a comparative study. BMC Bioinformatics 9(1):497","journal-title":"BMC Bioinformatics"},{"key":"365_CR11","first-page":"34","volume":"1","author":"B Desgraupes","year":"2013","unstructured":"Desgraupes B (2013) Clustering indices. University of Paris Ouest-Lab Modal\u2019X 1:34","journal-title":"University of Paris Ouest-Lab Modal\u2019X"},{"issue":"1","key":"365_CR12","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1186\/1471-2105-6-289","volume":"6","author":"V Di Ges\u00fa","year":"2005","unstructured":"Di Ges\u00fa V, Giancarlo R, Bosco GL, Raimondi A, Scaturro D (2005) Genclust: a genetic algorithm for clustering gene expression data. BMC Bioinformatics 6(1):289","journal-title":"BMC Bioinformatics"},{"issue":"25","key":"365_CR13","doi-asserted-by":"publisher","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","volume":"95","author":"MB Eisen","year":"1998","unstructured":"Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci 95(25):14863\u201314868","journal-title":"Proc Natl Acad Sci"},{"issue":"1","key":"365_CR14","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1186\/s12885-015-1190-4","volume":"15","author":"T Erbes","year":"2015","unstructured":"Erbes T, Hirschfeld M, R\u00fccker G, Jaeger M, Boas J, Iborra S, Mayer S, Gitsch G, Stickeler E (2015) Feasibility of urinary microrna detection in breast cancer patients and its potential as an innovative non-invasive biomarker. BMC Cancer 15(1):193","journal-title":"BMC Cancer"},{"issue":"12","key":"365_CR15","doi-asserted-by":"publisher","first-page":"2634","DOI":"10.1002\/ijc.30603","volume":"140","author":"M Fane","year":"2017","unstructured":"Fane M, Harris L, Smith AG, Piper M (2017) Nuclear factor one transcription factors as epigenetic regulators in cancer. Int J Cancer 140(12):2634\u20132641","journal-title":"Int J Cancer"},{"issue":"3","key":"365_CR16","first-page":"256","volume":"4","author":"N Goossens","year":"2015","unstructured":"Goossens N, Nakagawa S, Sun X, Hoshida Y (2015) Cancer biomarker discovery and validation. Trans Cancer Res 4(3):256","journal-title":"Trans Cancer Res"},{"issue":"1","key":"365_CR17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12890-019-1042-0","volume":"20","author":"L Han","year":"2020","unstructured":"Han L, Sheng B, Zeng Q, Yao W, Jiang Q (2020) Correlation between mmp2 expression in lung cancer tissues and clinical parameters: a retrospective clinical analysis. BMC Pulmonary Medi 20(1):1\u20139","journal-title":"BMC Pulmonary Medi"},{"issue":"1","key":"365_CR18","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/s13015-016-0085-5","volume":"11","author":"R Henriques","year":"2016","unstructured":"Henriques R, Madeira SC (2016) Bic2pam: constraint-guided biclustering for biological data analysis with domain knowledge. Algorithms Mol Biol 11(1):23","journal-title":"Algorithms Mol Biol"},{"issue":"2","key":"365_CR19","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1016\/j.molonc.2012.01.010","volume":"6","author":"NL Henry","year":"2012","unstructured":"Henry NL, Hayes DF (2012) Cancer biomarkers. Mol Oncol 6(2):140\u2013146","journal-title":"Mol Oncol"},{"issue":"2","key":"365_CR20","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1093\/bioinformatics\/17.2.126","volume":"17","author":"J Herrero","year":"2001","unstructured":"Herrero J, Valencia A, Dopazo J (2001) A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 17(2):126\u2013136","journal-title":"Bioinformatics"},{"issue":"10","key":"365_CR21","doi-asserted-by":"publisher","first-page":"1259","DOI":"10.1093\/bioinformatics\/btl065","volume":"22","author":"D Huang","year":"2006","unstructured":"Huang D, Pan W (2006) Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data. Bioinformatics 22(10):1259\u20131268","journal-title":"Bioinformatics"},{"issue":"9","key":"365_CR22","doi-asserted-by":"publisher","first-page":"R183","DOI":"10.1186\/gb-2007-8-9-r183","volume":"8","author":"DW Huang","year":"2007","unstructured":"Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA (2007) The david gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol 8(9):R183","journal-title":"Genome Biol"},{"issue":"2","key":"365_CR23","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1111\/j.2044-8317.1976.tb00714.x","volume":"29","author":"L Hubert","year":"1976","unstructured":"Hubert L, Schultz J (1976) Quadratic assignment as a general data analysis strategy. Br J Math Stat Psychol 29(2):190\u2013241","journal-title":"Br J Math Stat Psychol"},{"key":"365_CR24","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1016\/j.eswa.2016.02.029","volume":"55","author":"SF Hussain","year":"2016","unstructured":"Hussain SF, Ramazan M (2016) Biclustering of human cancer microarray data using co-similarity based co-clustering. Expert Syst Appl 55:520\u2013531","journal-title":"Expert Syst Appl"},{"issue":"Suppl 2","key":"365_CR25","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2105-15-S2-S2","volume":"15","author":"PA Jaskowiak","year":"2014","unstructured":"Jaskowiak PA, Campello RJ, Costa IG (2014) On the selection of appropriate distances for gene expression data clustering. BMC Bioinform 15(Suppl 2):S2","journal-title":"BMC Bioinform"},{"issue":"16","key":"365_CR26","doi-asserted-by":"publisher","first-page":"2711","DOI":"10.1093\/bioinformatics\/bth312","volume":"20","author":"L Ji","year":"2004","unstructured":"Ji L, Tan K-L (2004) Mining gene expression data for positive and negative co-regulated gene clusters. Bioinformatics 20(16):2711\u20132718","journal-title":"Bioinformatics"},{"issue":"11","key":"365_CR27","doi-asserted-by":"publisher","first-page":"1370","DOI":"10.1109\/TKDE.2004.68","volume":"16","author":"D Jiang","year":"2004","unstructured":"Jiang D, Tang C, Zhang A (2004) Cluster analysis for gene expression data: a survey. Knowl Data Eng IEEE Trans 16(11):1370\u20131386","journal-title":"Knowl Data Eng IEEE Trans"},{"issue":"1","key":"365_CR28","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1186\/s12911-016-0292-5","volume":"16","author":"S Joe","year":"2016","unstructured":"Joe S, Nam H (2016) Prognostic factor analysis for breast cancer using gene expression profiles. BMC Med Inform Decision Making 16(1):56","journal-title":"BMC Med Inform Decision Making"},{"issue":"18","key":"365_CR29","doi-asserted-by":"publisher","first-page":"4506","DOI":"10.3390\/ijms20184506","volume":"20","author":"K Juurikka","year":"2019","unstructured":"Juurikka K, Butler GS, Salo T, Nyberg P, \u00c5str\u00f6m P (2019) The role of mmp8 in cancer: a systematic review. Int J Mol Sci 20(18):4506","journal-title":"Int J Mol Sci"},{"issue":"3","key":"365_CR30","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1016\/j.compbiomed.2007.11.001","volume":"38","author":"G Kerr","year":"2008","unstructured":"Kerr G, Ruskin HJ, Crane M, Doolan P (2008) Techniques for clustering gene expression data. Comput Biol Med 38(3):283\u2013293","journal-title":"Comput Biol Med"},{"issue":"10","key":"365_CR31","doi-asserted-by":"publisher","first-page":"1329","DOI":"10.1089\/cmb.2010.0085","volume":"18","author":"H Kim","year":"2011","unstructured":"Kim H, Watkinson J, Anastassiou D (2011) Biomarker discovery using statistically significant gene sets. J Comput Biol 18(10):1329\u20131338","journal-title":"J Comput Biol"},{"key":"365_CR32","doi-asserted-by":"publisher","first-page":"4569","DOI":"10.2147\/OTT.S108485","volume":"9","author":"A Kulshrestha","year":"2016","unstructured":"Kulshrestha A, Suman S, Ranjan R (2016) Network analysis reveals potential markers for pediatric adrenocortical carcinoma. OncoTargets Therapy 9:4569","journal-title":"OncoTargets Therapy"},{"issue":"2","key":"365_CR33","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1038\/sj.onc.1209778","volume":"26","author":"P Laiho","year":"2007","unstructured":"Laiho P, Kokko A, Vanharanta S, Salovaara R, Sammalkorpi H, J\u00e4rvinen H, Mecklin J, Karttunen T, Tuppurainen K, Davalos V et al (2007) Serrated carcinomas form a subclass of colorectal cancer with distinct molecular basis. Oncogene 26(2):312\u2013320","journal-title":"Oncogene"},{"issue":"2","key":"365_CR34","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1007\/s12559-015-9349-5","volume":"8","author":"W-P Lee","year":"2016","unstructured":"Lee W-P, Lin C-H (2016) Combining expression data and knowledge ontology for gene clustering and network reconstruction. Cognit Comput 8(2):217\u2013227","journal-title":"Cognit Comput"},{"issue":"9","key":"365_CR35","doi-asserted-by":"publisher","first-page":"1172","DOI":"10.1200\/JCO.2012.44.3184","volume":"31","author":"Z Li","year":"2013","unstructured":"Li Z, Herold T, He C, Valk PJ, Chen P, Jurinovic V, Mansmann U, Radmacher MD, Maharry KS, Sun M et al (2013) Identification of a 24-gene prognostic signature that improves the european leukemianet risk classification of acute myeloid leukemia: an international collaborative study. J Clinical Oncol 31(9):1172\u20131181","journal-title":"J Clinical Oncol"},{"issue":"5","key":"365_CR36","first-page":"573","volume":"26","author":"W Li","year":"2014","unstructured":"Li W, Huang K, Guo H, Cui G, Zhao S (2014) Inhibition of non-small-cell lung cancer cell proliferation by pbx1. Chin J Cancer Res 26(5):573","journal-title":"Chin J Cancer Res"},{"key":"365_CR37","doi-asserted-by":"publisher","first-page":"781","DOI":"10.2147\/OTT.S144241","volume":"11","author":"L Li","year":"2018","unstructured":"Li L, Sun F, Chen X, Zhang M (2018) Isl1 is upregulated in breast cancer and promotes cell proliferation, invasion, and angiogenesis. OncoTargets Therapy 11:781","journal-title":"OncoTargets Therapy"},{"key":"365_CR38","doi-asserted-by":"publisher","first-page":"803","DOI":"10.3389\/fgene.2019.00803","volume":"10","author":"J Li","year":"2019","unstructured":"Li J, Ma S, Lin T, Li Y, Yang S, Zhang W, Zhang R, Wang Y (2019) Comprehensive analysis of therapy-related messenger rnas and long noncoding rnas as novel biomarkers for advanced colorectal cancer. Front Genet 10:803","journal-title":"Front Genet"},{"issue":"2","key":"365_CR39","doi-asserted-by":"publisher","first-page":"2075","DOI":"10.3892\/mmr.2017.6855","volume":"16","author":"W Lin","year":"2017","unstructured":"Lin W, Feng M, Li X, Zhong P, Guo A, Chen G, Xu Q, Ye Y (2017) Transcriptome profiling of cancer and normal tissues from cervical squamous cancer patients by deep sequencing. Mol Med Rep 16(2):2075\u20132088","journal-title":"Mol Med Rep"},{"issue":"1","key":"365_CR40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12935-020-01316-6","volume":"20","author":"Z Lin","year":"2020","unstructured":"Lin Z, Lin X, Zhu L, Huang J, Huang Y (2020) Trim2 directly deubiquitinates and stabilizes snail1 protein, mediating proliferation and metastasis of lung adenocarcinoma. Cancer Cell Int 20(1):1\u201314","journal-title":"Cancer Cell Int"},{"issue":"1","key":"365_CR41","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1186\/s12872-016-0217-3","volume":"16","author":"J Liu","year":"2016","unstructured":"Liu J, Jing L, Tu X (2016) Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease. BMC Cardiovascular Disorders 16(1):54","journal-title":"BMC Cardiovascular Disorders"},{"issue":"10","key":"365_CR42","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1093\/bioinformatics\/btg153","volume":"19","author":"PW Lord","year":"2003","unstructured":"Lord PW, Stevens RD, Brass A, Goble CA (2003) Investigating semantic similarity measures across the gene ontology: the relationship between sequence and annotation. Bioinformatics 19(10):1275\u20131283","journal-title":"Bioinformatics"},{"issue":"14","key":"365_CR43","doi-asserted-by":"publisher","first-page":"2138","DOI":"10.1016\/j.patrec.2010.01.006","volume":"31","author":"G Macintyre","year":"2010","unstructured":"Macintyre G, Bailey J, Gustafsson D, Haviv I, Kowalczyk A (2010) Using gene ontology annotations in exploratory microarray clustering to understand cancer etiology. Pattern Recognit Lett 31(14):2138\u20132146","journal-title":"Pattern Recognit Lett"},{"issue":"2","key":"365_CR44","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1109\/TCBB.2018.2820695","volume":"16","author":"K Mandal","year":"2018","unstructured":"Mandal K, Sarmah R, Bhattacharyya DK (2018) Biomarker identification for cancer disease using biclustering approach: an empirical study. IEEE\/ACM Trans Comput Biol Bioinform 16(2):490\u2013509","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"365_CR45","doi-asserted-by":"publisher","first-page":"11966","DOI":"10.1038\/srep11966","volume":"5","author":"E Martinez-Ledesma","year":"2015","unstructured":"Martinez-Ledesma E, Verhaak RG, Trevi\u00f1o V (2015) Identification of a multi-cancer gene expression biomarker for cancer clinical outcomes using a network-based algorithm. Sci Rep 5:11966","journal-title":"Sci Rep"},{"issue":"12","key":"365_CR46","doi-asserted-by":"publisher","first-page":"2464","DOI":"10.1016\/j.patcog.2006.03.003","volume":"39","author":"S Mitra","year":"2006","unstructured":"Mitra S, Banka H (2006) Multi-objective evolutionary biclustering of gene expression data. Pattern Recognit 39(12):2464\u20132477","journal-title":"Pattern Recognit"},{"issue":"6","key":"365_CR47","first-page":"1590","volume":"42","author":"S Mitra","year":"2012","unstructured":"Mitra S, Ghosh S (2012) Feature selection and clustering of gene expression profiles using biological knowledge, IEEE Transactions on Systems, Man, and Cybernetics. Part C (Applications and Reviews) 42(6):1590\u20131599","journal-title":"Part C (Applications and Reviews)"},{"issue":"49","key":"365_CR48","doi-asserted-by":"publisher","first-page":"85692","DOI":"10.18632\/oncotarget.21127","volume":"8","author":"A Mohammed","year":"2017","unstructured":"Mohammed A, Biegert G, Adamec J, Helikar T (2017) Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers. Oncotarget 8(49):85692","journal-title":"Oncotarget"},{"issue":"4","key":"365_CR49","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1007\/s10038-007-0119-4","volume":"52","author":"A Myoumoto","year":"2007","unstructured":"Myoumoto A, Nakatani K, Koshimizu T-A, Matsubara H, Adachi S, Tsujimoto G (2007) Glucocorticoid-induced granzyme a expression can be used as a marker of glucocorticoid sensitivity for acute lymphoblastic leukemia therapy. J Human Genet 52(4):328\u2013333","journal-title":"J Human Genet"},{"issue":"3","key":"365_CR50","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1016\/j.cmpb.2015.02.010","volume":"119","author":"JA Nepomuceno","year":"2015","unstructured":"Nepomuceno JA, Troncoso A, Nepomuceno-Chamorro IA, Aguilar-Ruiz JS (2015) Integrating biological knowledge based on functional annotations for biclustering of gene expression data. Comput Methods Programs Biomed 119(3):163\u2013180","journal-title":"Comput Methods Programs Biomed"},{"issue":"4","key":"365_CR51","first-page":"394","volume":"38","author":"Y-L Pan","year":"2018","unstructured":"Pan Y-L, Jun Q, Zhou L, Zhang T-T, Qiang L (2018) Ribosomal protein 16 overexpresses in prostate cancer and promotes tumor progression. J Shanghai Jiaotong Univ (Med Sci) 38(4):394\u2013399","journal-title":"J Shanghai Jiaotong Univ (Med Sci)"},{"issue":"7","key":"365_CR52","doi-asserted-by":"publisher","first-page":"e1000443","DOI":"10.1371\/journal.pcbi.1000443","volume":"5","author":"C Pesquita","year":"2009","unstructured":"Pesquita C, Faria D, Falcao AO, Lord P, Couto FM (2009) Semantic similarity in biomedical ontologies. PLoS Comput Biol 5(7):e1000443","journal-title":"PLoS Comput Biol"},{"issue":"12","key":"365_CR53","doi-asserted-by":"publisher","first-page":"3046","DOI":"10.1016\/j.cor.2012.03.008","volume":"39","author":"H Pirim","year":"2012","unstructured":"Pirim H, Ek\u015fio\u011flu B, Perkins AD, Y\u00fcceer \u00c7 (2012) Clustering of high throughput gene expression data. Comput Oper Res 39(12):3046\u20133061","journal-title":"Comput Oper Res"},{"issue":"26","key":"365_CR54","doi-asserted-by":"publisher","first-page":"15149","DOI":"10.1073\/pnas.211566398","volume":"98","author":"S Ramaswamy","year":"2001","unstructured":"Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang C-H, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP et al (2001) Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci 98(26):15149\u201315154","journal-title":"Proc Natl Acad Sci"},{"issue":"11","key":"365_CR55","doi-asserted-by":"publisher","first-page":"2210","DOI":"10.1109\/5.726788","volume":"86","author":"K Rose","year":"1998","unstructured":"Rose K (1998) Deterministic annealing for clustering, compression, classification, regression, and related optimization problems. Proc IEEE 86(11):2210\u20132239","journal-title":"Proc IEEE"},{"issue":"1","key":"365_CR56","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1186\/s12859-015-0565-5","volume":"16","author":"V Sachnev","year":"2015","unstructured":"Sachnev V, Saraswathi S, Niaz R, Kloczkowski A, Suresh S (2015) Multi-class bcga-elm based classifier that identifies biomarkers associated with hallmarks of cancer. BMC Bioinform 16(1):166","journal-title":"BMC Bioinform"},{"issue":"1","key":"365_CR57","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1186\/1742-4682-9-34","volume":"9","author":"NMA Samee","year":"2012","unstructured":"Samee NMA, Solouma NH, Kadah YM (2012) Detection of biomarkers for hepatocellular carcinoma using a hybrid univariate gene selection methods. Theoretical Biol Med Modell 9(1):34","journal-title":"Theoretical Biol Med Modell"},{"issue":"2","key":"365_CR58","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1016\/S1535-6108(02)00030-2","volume":"1","author":"D Singh","year":"2002","unstructured":"Singh D, Febbo PG, Ross K, Jackson DG, Manola J, Ladd C, Tamayo P, Renshaw AA, D\u2019Amico AV, Richie JP et al (2002) Gene expression correlates of clinical prostate cancer behavior. Cancer cell 1(2):203\u2013209","journal-title":"Cancer cell"},{"issue":"7","key":"365_CR59","doi-asserted-by":"publisher","first-page":"e1000307","DOI":"10.1371\/journal.pmed.1000307","volume":"7","author":"JK Stratford","year":"2010","unstructured":"Stratford JK, Bentrem DJ, Anderson JM, Fan C, Volmar KA, Marron J, Routh ED, Caskey LS, Samuel JC, Der CJ et al (2010) A six-gene signature predicts survival of patients with localized pancreatic ductal adenocarcinoma. PLoS Med 7(7):e1000307","journal-title":"PLoS Med"},{"issue":"6","key":"365_CR60","doi-asserted-by":"publisher","first-page":"2907","DOI":"10.1073\/pnas.96.6.2907","volume":"96","author":"P Tamayo","year":"1999","unstructured":"Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci 96(6):2907\u20132912","journal-title":"Proc Natl Acad Sci"},{"issue":"3","key":"365_CR61","doi-asserted-by":"publisher","first-page":"e0152333","DOI":"10.1371\/journal.pone.0152333","volume":"11","author":"P Tellaroli","year":"2016","unstructured":"Tellaroli P, Bazzi M, Donato M, Brazzale AR, Dr\u0103ghici S (2016) Cross-clustering: a partial clustering algorithm with automatic estimation of the number of clusters. PloS one 11(3):e0152333","journal-title":"PloS one"},{"issue":"9","key":"365_CR62","doi-asserted-by":"publisher","first-page":"5116","DOI":"10.1073\/pnas.091062498","volume":"98","author":"VG Tusher","year":"2001","unstructured":"Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci 98(9):5116\u20135121","journal-title":"Proc Natl Acad Sci"},{"issue":"10","key":"365_CR63","doi-asserted-by":"publisher","first-page":"1274","DOI":"10.1093\/bioinformatics\/btm087","volume":"23","author":"JZ Wang","year":"2007","unstructured":"Wang JZ, Du Z, Payattakool R, Yu PS, Chen C-F (2007) A new method to measure the semantic similarity of go terms. Bioinformatics 23(10):1274\u20131281","journal-title":"Bioinformatics"},{"issue":"10","key":"365_CR64","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1093\/bioinformatics\/bts129","volume":"28","author":"H Yang","year":"2012","unstructured":"Yang H, Nepusz T, Paccanaro A (2012) Improving go semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty. Bioinformatics 28(10):1383\u20131389","journal-title":"Bioinformatics"},{"issue":"7","key":"365_CR65","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1093\/bioinformatics\/btq064","volume":"26","author":"G Yu","year":"2010","unstructured":"Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S (2010) Gosemsim: an r package for measuring semantic similarity among go terms and gene products. Bioinformatics 26(7):976\u2013978","journal-title":"Bioinformatics"},{"issue":"1","key":"365_CR66","first-page":"917","volume":"15","author":"G Yu","year":"2018","unstructured":"Yu G, Yin C, Jiang L, Xu D, Zheng Z, Wang Z, Wang C, Zhou H, Jiang X, Liu Q et al (2018) Amyloid precursor protein has clinical and prognostic significance in aml1-eto-positive acute myeloid leukemia. Oncol Lett 15(1):917\u2013925","journal-title":"Oncol Lett"},{"issue":"16","key":"365_CR67","doi-asserted-by":"publisher","first-page":"2953","DOI":"10.7150\/jca.25542","volume":"9","author":"Y Yu","year":"2018","unstructured":"Yu Y, Liu D, Liu Z, Li S, Ge Y, Sun W, Liu B (2018) The inhibitory effects of col1a2 on colorectal cancer cell proliferation, migration, and invasion. J Cancer 9(16):2953","journal-title":"J Cancer"},{"key":"365_CR68","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/j.compbiomed.2014.01.014","volume":"47","author":"W Zhou","year":"2014","unstructured":"Zhou W, Dickerson JA (2014) A novel class dependent feature selection method for cancer biomarker discovery. Comput Biol Med 47:66\u201375","journal-title":"Comput Biol Med"},{"issue":"5","key":"365_CR69","doi-asserted-by":"publisher","first-page":"1973","DOI":"10.1159\/000479837","volume":"42","author":"G-Z Zhu","year":"2017","unstructured":"Zhu G-Z, Yang Y-L, Zhang Y-J, Liu W, Li M-P, Zeng W-J, Zhao X-L, Chen X-P (2017) High expression of ahsp, epb42, gypc and hemgn predicts favorable prognosis in flt3-itd-negative acute myeloid leukemia. Cell Physiol Biochem 42(5):1973\u20131984","journal-title":"Cell Physiol Biochem"},{"key":"365_CR70","doi-asserted-by":"crossref","unstructured":"Adryan B, Schuh R (2004) Gene-ontology-based clustering of gene expression data, Bioinformatics 20(16):2851\u20132852. http:\/\/dx.doi.org\/10.1093\/bioinformatics\/bth289","DOI":"10.1093\/bioinformatics\/bth289"},{"key":"365_CR71","unstructured":"Ball GH, Hall DJ (1965) Isodata, a novel method of data analysis and pattern classification. Tech. rep, Stanford research inst Menlo Park CA"},{"key":"365_CR72","unstructured":"Bellaachia A, Portnoy D, Chen Y, Elkahloun AG (2002) E-cast: a data mining algorithm for gene expression data., in: BIOKDD, pp. 49\u201354"},{"key":"365_CR73","doi-asserted-by":"crossref","unstructured":"Binns D, Dimmer E, Huntley R, Barrell D, O\u2019donovan C, Apweiler R (2009) Quickgo: a web-based tool for gene ontology searching, Bioinformatics 25(22):3045\u20133046","DOI":"10.1093\/bioinformatics\/btp536"},{"key":"365_CR74","doi-asserted-by":"crossref","unstructured":"Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A (2018) Global cancer statistics 2018: Globocan estimates of incidence and mortality worldwide for 36 cancers in 185 countries, CA: a cancer journal for clinicians 68(6):394\u2013424","DOI":"10.3322\/caac.21492"},{"key":"365_CR75","doi-asserted-by":"crossref","unstructured":"Couto FM, Silva MJ, Coutinho PM (2005) Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors, in: Proceedings of the 14th ACM international conference on Information and knowledge management, pp. 343\u2013344","DOI":"10.1145\/1099554.1099658"},{"key":"365_CR76","doi-asserted-by":"crossref","unstructured":"Davies DL, Bouldin DW (1979) A cluster separation measure, IEEE transactions on pattern analysis and machine intelligence (2):224\u2013227","DOI":"10.1109\/TPAMI.1979.4766909"},{"key":"365_CR77","unstructured":"Ester M, Kriegel H-P, Sander J, Xu X (1996) A density-based algorithm for discovering clusters in large spatial databases with noise., in: Kdd, Vol.&nbsp;96, pp. 226\u2013231"},{"key":"365_CR78","doi-asserted-by":"crossref","unstructured":"Hang S, You Z, Chun LY (2009) Incorporating biological knowledge into density-based clustering analysis of gene expression data, in: Fuzzy Systems and Knowledge Discovery, 2009. FSKD\u201909. Sixth International Conference on, Vol.&nbsp;5, IEEE, pp. 52\u201356","DOI":"10.1109\/FSKD.2009.191"},{"key":"365_CR79","doi-asserted-by":"crossref","unstructured":"Jaskowiak PA, Campello RJ, Costa Filho IG (2013) Proximity measures for clustering gene expression microarray data: a validation methodology and a comparative analysis, IEEE\/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 10(4):845\u2013857","DOI":"10.1109\/TCBB.2013.9"},{"key":"365_CR80","unstructured":"Jiang JJ, Conrath DW, Semantic similarity based on corpus statistics and lexical taxonomy, arXiv preprint cmp-lg\/9709008"},{"key":"365_CR81","unstructured":"Jiang D, Pei J, Zhang A (2003) Dhc: a density-based hierarchical clustering method for time series gene expression data, in: Bioinformatics and Bioengineering, 2003. Proceedings. Third IEEE Symposium on, IEEE, pp. 393\u2013400"},{"key":"365_CR82","doi-asserted-by":"crossref","unstructured":"Jiang D, Pei J, Zhang A (2004) Gpx: interactive mining of gene expression data, in: Proceedings of the Thirtieth international conference on Very large data bases-Volume 30, VLDB Endowment, pp. 1249\u20131252","DOI":"10.1016\/B978-012088469-8.50119-4"},{"key":"365_CR83","doi-asserted-by":"crossref","unstructured":"Lam Y, Tsang PW, Leung C (2013) Pso-based k-means clustering with enhanced cluster matching for gene expression data, Neural Comput Appl 22(7-8):1349\u20131355. http:\/\/dx.doi.org\/10.1007\/s00521-012-0959-5","DOI":"10.1007\/s00521-012-0959-5"},{"key":"365_CR84","doi-asserted-by":"crossref","unstructured":"Li W-h, Zhang H, Guo Q, Wu X-d, Xu Z-s, Dang C-x, Xia P, Song Y-c (2015) Detection of snca and fbn1 methylation in the stool as a biomarker for colorectal cancer, Disease markers","DOI":"10.1155\/2015\/657570"},{"key":"365_CR85","unstructured":"Lin D (1998) An information-theoretic definition of similarity, in: J.&nbsp;W. Shavlik (Ed.), Proceedings of the Fifteenth International Conference on Machine Learning (ICML 1998), Madison, Wisconsin, USA, Morgan Kaufmann, 1998, pp. 296\u2013304"},{"key":"365_CR86","unstructured":"Liu J, Wang W, Yang J (2004) Gene ontology friendly biclustering of expression profiles, in: Computational Systems Bioinformatics Conference. CSB 2004. Proceedings. 2004 IEEE, IEEE, 2004, pp. 436\u2013447"},{"key":"365_CR87","doi-asserted-by":"crossref","unstructured":"Lu Y, Lu S, Fotouhi F, Deng Y, Brown SJ (2004) Incremental genetic k-means algorithm and its application in gene expression data analysis, BMC Bioinformatics 5:172. http:\/\/dx.doi.org\/10.1186\/1471-2105-5-172","DOI":"10.1186\/1471-2105-5-172"},{"key":"365_CR88","unstructured":"MacQueen J et&nbsp;al. (1967) Some methods for classification and analysis of multivariate observations. In: Proceedings of the fifth Berkeley symposium on mathematical statistics and probability, Vol.&nbsp;1, Oakland, CA, USA, pp. 281\u2013297"},{"key":"365_CR89","doi-asserted-by":"crossref","unstructured":"Mandal K, Sarmah R (2018) A density-based clustering for gene expression data using gene ontology, in: Proceedings of the International Conference on Computing and Communication Systems, Springer, pp. 757\u2013765","DOI":"10.1007\/978-981-10-6890-4_72"},{"key":"365_CR90","doi-asserted-by":"crossref","unstructured":"Ovaska K, Laakso M, Hautaniemi S (2008) Fast gene ontology based clustering for microarray experiments, BioData Mining 1. http:\/\/dx.doi.org\/10.1186\/1756-0381-1-11","DOI":"10.1186\/1756-0381-1-11"},{"key":"365_CR91","doi-asserted-by":"crossref","unstructured":"Oyelade J, Isewon I, Oladipupo F, Aromolaran O, Uwoghiren E, Ameh F, Achas M, Adebiyi E (2016) Clustering algorithms: their application to gene expression data, Bioinformatics and Biology insights 10:BBI\u2013S38316","DOI":"10.4137\/BBI.S38316"},{"key":"365_CR92","doi-asserted-by":"crossref","unstructured":"Pesquita C (2017) Semantic similarity in the gene ontology, in: The gene ontology handbook, Humana Press, New York, NY, pp. 161\u2013173","DOI":"10.1007\/978-1-4939-3743-1_12"},{"key":"365_CR93","unstructured":"Resnik P, Using information content to evaluate semantic similarity in a taxonomy, arXiv preprint cmp-lg\/9511007"},{"key":"365_CR94","unstructured":"Sharan R, Shamir R (2000) Click: a clustering algorithm with applications to gene expression analysis. In: Proc Int Conf Intell Syst Mol Biol, Vol.&nbsp;8:16"},{"key":"365_CR95","doi-asserted-by":"crossref","unstructured":"Sheng W, Tucker A, Liu X (2010) A niching genetic k-means algorithm and its applications to gene expression data, Soft Comput. 14(1):9\u201319. http:\/\/dx.doi.org\/10.1007\/s00500-008-0386-9","DOI":"10.1007\/s00500-008-0386-9"},{"key":"365_CR96","doi-asserted-by":"crossref","unstructured":"Speer N, Spieth C, Zell A (2004) A memetic clustering algorithm for the functional partition of genes based on the gene ontology, in: Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2004, La Jolla, CA, USA, pp. 252\u2013259. http:\/\/dx.doi.org\/10.1109\/CIBCB.2004.1393961","DOI":"10.1109\/CIBCB.2004.1393961"},{"key":"365_CR97","doi-asserted-by":"crossref","unstructured":"Srivastava S, Zhang L, Jin R, Chan C, A novel method incorporating gene ontology information for unsupervised clustering and feature selection, PloS one 3(12)","DOI":"10.1371\/journal.pone.0003860"},{"key":"365_CR98","doi-asserted-by":"crossref","unstructured":"Verbanck M, L\u00ea S, Pag\u00e8s J (2013) A new unsupervised gene clustering algorithm based on the integration of biological knowledge into expression data, BMC Bioinformatics 14:42. http:\/\/dx.doi.org\/10.1186\/1471-2105-14-42","DOI":"10.1186\/1471-2105-14-42"},{"key":"365_CR99","doi-asserted-by":"crossref","unstructured":"Wu F (2008) Genetic weighted k-means algorithm for clustering large-scale gene expression data, BMC Bioinformatics 9(S-6). http:\/\/dx.doi.org\/10.1186\/1471-2105-9-S6-S12","DOI":"10.1186\/1471-2105-9-S6-S12"},{"key":"365_CR100","unstructured":"Xu X, Lu Y, Tung AK, Wang W (2006) Mining shifting-and-scaling co-regulation patterns on gene expression profiles, in: 22nd International Conference on Data Engineering (ICDE\u201906), IEEE, pp. 89\u201389"},{"key":"365_CR101","doi-asserted-by":"crossref","unstructured":"Zhou X, Sun H, Wang D-P, Zhang Y, Zhou Y (2010) Analysis of gene expression data based on density and biological knowledge, in: 2010 Fifth International Conference on Frontier of Computer Science and Technology, IEEE, pp. 448\u2013453","DOI":"10.1109\/FCST.2010.97"}],"container-title":["Network Modeling Analysis in Health Informatics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s13721-022-00365-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s13721-022-00365-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s13721-022-00365-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,3]],"date-time":"2022-12-03T08:34:17Z","timestamp":1670056457000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s13721-022-00365-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,21]]},"references-count":101,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2022,12]]}},"alternative-id":["365"],"URL":"https:\/\/doi.org\/10.1007\/s13721-022-00365-3","relation":{},"ISSN":["2192-6662","2192-6670"],"issn-type":[{"type":"print","value":"2192-6662"},{"type":"electronic","value":"2192-6670"}],"subject":[],"published":{"date-parts":[[2022,6,21]]},"assertion":[{"value":"24 September 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 May 2022","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 May 2022","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 June 2022","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"24"}}