Lazareva O, Canzar S, Yuan K, Baumbach J, Blumenthal DB, Tieri P, Kacprowski T, List M (2020)
Publication Type: Journal article
Publication year: 2020
Original Authors: Olga Lazareva, Stefan Canzar, Kevin Yuan, Jan Baumbach, David B Blumenthal, Paolo Tieri, Tim Kacprowski, Markus List
Book Volume: 37
Pages Range: 2398 - 2404
Journal Issue: 16
DOI: 10.1093/bioinformatics/btaa1076
Unsupervised learning approaches are frequently employed to stratify patients into clinically relevant subgroups and to identify biomarkers such as disease-associated genes. However, clustering and biclustering techniques are oblivious to the functional relationship of genes and are thus not ideally suited to pinpoint molecular mechanisms along with patient subgroups.
We developed the network-constrained biclustering approach BiCoN (Biclustering Constrained by Networks) which (i) restricts biclusters to functionally related genes connected in molecular interaction networks and (ii) maximizes the difference in gene expression between two subgroups of patients. This allows BiCoN to simultaneously pinpoint molecular mechanisms responsible for the patient grouping. Network-constrained clustering of genes makes BiCoN more robust to noise and batch effects than typical clustering and biclustering methods. BiCoN can faithfully reproduce known disease subtypes as well as novel, clinically relevant patient subgroups, as we could demonstrate using breast and lung cancer datasets. In summary, BiCoN is a novel systems medicine tool that combines several heuristic optimization strategies for robust disease mechanism extraction. BiCoN is well-documented and freely available as a python package or a web interface.
PyPI package: https://pypi.org/project/bicon
Supplementary data are available at Bioinformatics online.
APA:
Lazareva, O., Canzar, S., Yuan, K., Baumbach, J., Blumenthal, D.B., Tieri, P.,... List, M. (2020). BiCoN: Network-constrained biclustering of patients and omics data. Bioinformatics, 37(16), 2398 - 2404. https://dx.doi.org/10.1093/bioinformatics/btaa1076
MLA:
Lazareva, Olga, et al. "BiCoN: Network-constrained biclustering of patients and omics data." Bioinformatics 37.16 (2020): 2398 - 2404.
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