A model-based clustering algorithm with covariates adjustment and its application to lung cancer stratification

Relvas, Carlos E. M.1; Nakata, Asuka2; Chen, Guoan3; Beer, David G.4; Gotoh, Noriko2; Fujita, Andre1

2023-09-01

10.1142/S0219720023500191

JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY   Impact Factor & Quartile

0219-7200

1757-6334

Usually, the clustering process is the first step in several data analyses. Clustering allows identify patterns we did not note before and helps raise new hypotheses. However, one challenge when analyzing empirical data is the presence of covariates, which may mask the obtained clustering structure. For example, suppose we are interested in clustering a set of individuals into controls and cancer patients. A clustering algorithm could group subjects into young and elderly in this case. It may happen because the age at diagnosis is associated with cancer. Thus, we developed CEM-Co, a model-based clustering algorithm that removes/minimizes undesirable covariates' effects during the clustering process. We applied CEM-Co on a gene expression dataset composed of 129 stage I non-small cell lung cancer patients. As a result, we identified a subgroup with a poorer prognosis, while standard clustering algorithms failed.

Mixture Gaussian models EM algorithm clustering lung cancer

SCI

English

Others

Sao Paulo Research Foundation[FAPESP2018/21934-5] ; MEXT[15K18426] ; NCI[P30CA046592] ; JST[12103436] ; FAPESP["2018/17996-5","306811/2022-7"] ; CNPq[001] ; null[2018/21934-5]

Biochemistry & Molecular Biology ; Computer Science ; Mathematical & Computational Biology

Biochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology

WOS:001065378700002

WORLD SCIENTIFIC PUBL CO PTE LTD

Web of Science

1.Univ Sao Paulo, Inst Math & Stat, Rua Matao 1010, BR-05508090 Sao Paulo, SP, Brazil
2.Kanazawa Univ, Canc Res Inst, Kanazawa, Ishikawa 9201164, Japan
3.Southern Univ Sci & Technol, Sch Med, 1088 Xueyuan Blvd, Shenzhen 518055, Guangdong, Peoples R China
4.Univ Michigan, Rogel Canc Ctr, 1500 E Med Ctr Dr, Ann Arbor, MI 48109 USA

Relvas, Carlos E. M.,Nakata, Asuka,Chen, Guoan,et al. A model-based clustering algorithm with covariates adjustment and its application to lung cancer stratification[J]. JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY,2023.

Relvas, Carlos E. M.,Nakata, Asuka,Chen, Guoan,Beer, David G.,Gotoh, Noriko,&Fujita, Andre.(2023).A model-based clustering algorithm with covariates adjustment and its application to lung cancer stratification.JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY.

Relvas, Carlos E. M.,et al."A model-based clustering algorithm with covariates adjustment and its application to lung cancer stratification".JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (2023).