IKAP—Identifying K mAjor cell Population groups in single-cell RNA-sequencing analysis
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Abstract
Background
In single-cell RNA-sequencing analysis, clustering cells into groups and differentiating cell groups by differentially expressed (DE) genes are 2 separate steps for investigating cell identity. However, the ability to differentiate between cell groups could be affected by clustering. This interdependency often creates a bottleneck in the analysis pipeline, requiring researchers to repeat these 2 steps multiple times by setting different clustering parameters to identify a set of cell groups that are more differentiated and biologically relevant.
Findings
To accelerate this process, we have developed IKAP—an algorithm to identify major cell groups and improve differentiating cell groups by systematically tuning parameters for clustering. We demonstrate that, with default parameters, IKAP successfully identifies major cell types such as T cells, B cells, natural killer cells, and monocytes in 2 peripheral blood mononuclear cell datasets and recovers major cell types in a previously published mouse cortex dataset. These major cell groups identified by IKAP present more distinguishing DE genes compared with cell groups generated by different combinations of clustering parameters. We further show that cell subtypes can be identified by recursively applying IKAP within identified major cell types, thereby delineating cell identities in a multi-layered ontology.
Conclusions
By tuning the clustering parameters to identify major cell groups, IKAP greatly improves the automation of single-cell RNA-sequencing analysis to produce distinguishing DE genes and refine cell ontology using single-cell RNA-sequencing data.
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Now published in GigaScience doi: 10.1093/gigascience/giz121
Yun-Ching Chen 1Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAbhilash Suresh 1Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChingiz Underbayev 2Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteClare Sun 2Hematology Branch, National …
Now published in GigaScience doi: 10.1093/gigascience/giz121
Yun-Ching Chen 1Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAbhilash Suresh 1Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChingiz Underbayev 2Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteClare Sun 2Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKomudi Singh 1Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFayaz Seifuddin 1Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAdrian Wiestner 2Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMehdi Pirooznia 1Bioinformatics and Computational Biology Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United StatesFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: mehdi.pirooznia@nih.gov
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz121 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101927 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101928 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101929
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