UNVEILING CELLULAR DIVERSITY: A COMPREHENSIVE GUIDE TO CELL CLUSTERING METHODS
DOI:
https://doi.org/10.53555/eijbms.v8i4.156Keywords:
Cell Clustering, Cellular Diversity, Single-Cell Analysis, Clustering Techniques, Heterogeneity AnalysisAbstract
The study of cellular diversity has become increasingly critical in various fields of biology, including genomics, single-cell analysis, immunology, and cancer research. Cell clustering methods play a pivotal role in understanding and characterizing this diversity, enabling the identification of distinct cell populations within complex tissues and heterogeneous samples. This comprehensive guide aims to provide an overview of various cell clustering techniques, offering researchers a roadmap to navigate the intricacies of cellular heterogeneity analysis. In this guide, we begin by outlining the importance of cell clustering in elucidating cellular heterogeneity and its implications for biological research. We then discuss the foundational principles behind cell clustering methods, covering the broad spectrum of techniques, including traditional clustering algorithms, dimensionality reduction methods, and machine learning approaches. The guide delves into the practical aspects of data preprocessing, feature selection, and quality control, all of which are crucial steps before embarking on cell clustering. We also examine the specific challenges and considerations when dealing with single-cell RNA-sequencing data, which has emerged as a cornerstone technology in the study of cellular diversity. Throughout the guide, we emphasize the importance of selecting appropriate clustering methods based on the research objectives, data characteristics, and biological context. We discuss various validation strategies and visualization tools to assess the quality and interpretability of clustering results.
References
S. Miravet‐Verde et al., "Unraveling the hidden universe of small proteins in bacterial genomes," Molecular systems biology, vol. 15, no. 2, p. e8290, 2019.
G. R. R. Dewa, C. Park, and I. Sohn, "Distributed cell clustering based on multi-layer message passing for downlink joint processing coordinated multipoint transmission," Applied Sciences, vol. 10, no. 15, p. 5154, 2020.
I. Kela, "Unraveling Biological Information from Gene Expression Data, Using Advanced Clustering Techniques," M. Sc. thesis (Weizmann Institute of Science, 2001). Available at http://www …, 2001.
V. Raghavan and J. Ding, "Harnessing Agent-Based Modeling in CellAgentChat to Unravel Cell-Cell Interactions from Single-Cell Data," bioRxiv, p. 2023.08. 23.554489, 2023.
J.-F. Poulin, B. Tasic, J. Hjerling-Leffler, J. M. Trimarchi, and R. Awatramani, "Disentangling neural cell diversity using single-cell transcriptomics," Nature Neuroscience, vol. 19, no. 9, pp. 1131-1141, 2016.
N. R. Tucker et al., "Transcriptional and cellular diversity of the human heart," Circulation, vol. 142, no. 5, pp. 466-482, 2020.
C. Botta et al., "FlowCT for the analysis of large immunophenotypic data sets and biomarker discovery in cancer immunology," Blood Advances, vol. 6, no. 2, pp. 690-703, 2022.
F. Abram, "Systems-based approaches to unravel multi-species microbial community functioning," Computational and structural biotechnology journal, vol. 13, pp. 24-32, 2015.
A. Little, Y. Xie, and Q. Sun, "An analysis of classical multidimensional scaling with applications to clustering," Information and Inference: A Journal of the IMA, vol. 12, no. 1, pp. 72-112, 2023.
K. V. Solomon, C. H. Haitjema, D. A. Thompson, and M. A. O’Malley, "Extracting data from the muck: deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing," Current opinion in biotechnology, vol. 28, pp. 103-110, 2014.