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

Author(s)

Relvas, Carlos E. M. ; Nakata, Asuka ; Chen, Guoan ; Beer, David G. ; Gotoh, Noriko ; Fujita, Andre

• Document type: Journal article
• Source: JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY; v. 21, n. 04, p. 26-pg., 2023-09-08.

Abstract

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. (AU)

• FAPESP's process: 18/21934-5 - Network statistics: theory, methods, and applications
• Grantee: André Fujita
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 18/17996-5 - Stratification of psychiatric disorders by using network discriminant and clustering analyses
• Grantee: André Fujita
• Support Opportunities: Scholarships abroad - Research