Unsupervised single-cell analysis in triple-negative breast cancer

A case study

Arjun P. Athreya, Alan J. Gaglio, Zbigniew T. Kalbarczyk, Ravishankar K. Iyer, Junmei Cairns, Krishna R Kalari, Richard M Weinshilboum, Liewei M Wang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

This paper demonstrates an unsupervised learning approach to identify genes with significant differential expression across single-cell subpopulations induced by therapeutic treatment. Identifying this set of genes makes it possible to use well-established bioinformatics approaches such as pathway analysis to establish their biological relevance. Then, a biologist can use his/her prior knowledge to investigate in the laboratory, a few particular candidates among the subset of genes overlapping with relevant pathways. Due to the large size of the human genome and limitations in cost and skilled resources, biologists benefit from analytical methods combined with pathway analysis to design laboratory experiments focusing on only a few significant genes. As an example, we show how model-based unsupervised methods can identify a small set of genes (1% of the genome) that have significant differential expression in single-cells and are also highly correlated to pathways (p-value < 1E - 7) with anticancer effects driven by the antidiabetic drug metformin. Further analysis of genes on these relevant pathways reveal three candidate genes previously implicated in several anticancer mechanisms in other cancers, not driven by metformin. Identification of these genes can help biologists and clinicians design laboratory experiments to establish the molecular mechanisms of metformin in triple-negative breast cancer. In a domain where there is no prior knowledge of small biologically significant data, we demonstrate that careful data-driven methods can infer such significant small data to explain biological mechanisms.

Original languageEnglish (US)
Title of host publicationProceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages556-563
Number of pages8
ISBN (Electronic)9781509016105
DOIs
StatePublished - Jan 17 2017
Event2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 - Shenzhen, China
Duration: Dec 15 2016Dec 18 2016

Other

Other2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
CountryChina
CityShenzhen
Period12/15/1612/18/16

Fingerprint

Triple Negative Breast Neoplasms
Single-Cell Analysis
Genes
Metformin
Overlapping Genes
Human Genome
Computational Biology
Hypoglycemic Agents
Unsupervised learning
Bioinformatics
Learning
Genome
Costs and Cost Analysis
Experiments

ASJC Scopus subject areas

  • Genetics
  • Medicine (miscellaneous)
  • Genetics(clinical)
  • Biochemistry, medical
  • Biochemistry
  • Molecular Medicine
  • Health Informatics

Cite this

Athreya, A. P., Gaglio, A. J., Kalbarczyk, Z. T., Iyer, R. K., Cairns, J., Kalari, K. R., ... Wang, L. M. (2017). Unsupervised single-cell analysis in triple-negative breast cancer: A case study. In Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 (pp. 556-563). [7822581] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2016.7822581

Unsupervised single-cell analysis in triple-negative breast cancer : A case study. / Athreya, Arjun P.; Gaglio, Alan J.; Kalbarczyk, Zbigniew T.; Iyer, Ravishankar K.; Cairns, Junmei; Kalari, Krishna R; Weinshilboum, Richard M; Wang, Liewei M.

Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. Institute of Electrical and Electronics Engineers Inc., 2017. p. 556-563 7822581.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Athreya, AP, Gaglio, AJ, Kalbarczyk, ZT, Iyer, RK, Cairns, J, Kalari, KR, Weinshilboum, RM & Wang, LM 2017, Unsupervised single-cell analysis in triple-negative breast cancer: A case study. in Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016., 7822581, Institute of Electrical and Electronics Engineers Inc., pp. 556-563, 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Shenzhen, China, 12/15/16. https://doi.org/10.1109/BIBM.2016.7822581
Athreya AP, Gaglio AJ, Kalbarczyk ZT, Iyer RK, Cairns J, Kalari KR et al. Unsupervised single-cell analysis in triple-negative breast cancer: A case study. In Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. Institute of Electrical and Electronics Engineers Inc. 2017. p. 556-563. 7822581 https://doi.org/10.1109/BIBM.2016.7822581
Athreya, Arjun P. ; Gaglio, Alan J. ; Kalbarczyk, Zbigniew T. ; Iyer, Ravishankar K. ; Cairns, Junmei ; Kalari, Krishna R ; Weinshilboum, Richard M ; Wang, Liewei M. / Unsupervised single-cell analysis in triple-negative breast cancer : A case study. Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 556-563
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