Scina: Semi-supervised analysis of single cells in silico

Ze Zhang, Danni Luo, Xue Zhong, Jin Huk Choi, Yuanqing Ma, Stacy Wang, Elena Mahrt, Wei Guo, Eric W. Stawiski, Zora Modrusan, Somasekar Seshagiri, Payal Kapur, Gary C. Hon, James Brugarolas, Tao Wang

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

Advances in single-cell RNA sequencing (scRNA-Seq) have allowed for comprehensive analyses of single cell data. However, current analyses of scRNA-Seq data usually start from unsupervised clustering or visualization. These methods ignore the prior knowledge of transcriptomes and of the probable structures of the data. Moreover, cell identification heavily relies on subjective and inaccurate human inspection afterwards. To address these analytical challenges, we developed the Semi-supervised Category Identification and Assignment (SCINA) algorithm, a semi-supervised model, for analyses of scRNA-Seq and flow cytometry/CyTOF data, and other data of similar format, by automatically exploiting previously established gene signatures using an expectation–maximization (EM) algorithm. We applied SCINA on a wide range of datasets, and showed its accuracy, stableness and efficiency exceeded most popular unsupervised approaches. SCINA discovered an intermediate stage of oligodendrocyte from mouse brain scRNA-Seq data. SCINA also detected immune cell population shifting in Stk4 knock-out-knockoutmouse cytometry data. Finally, SCINA identified a new kidney tumor clade with similarity to FH-deficient tumors from bulk tumor data. Overall, SCINA provides both methodological advances and biological insights from perspectives different from traditional analytical methods.

Original languageEnglish (US)
Article number531
JournalGenes
Volume10
Issue number7
DOIs
StatePublished - Jul 1 2019

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Keywords

  • CyTOF
  • Fumarase
  • Fumarate hydratase
  • HLRCC
  • RCC
  • Renal cell carcinoma
  • SCINA
  • Single-cell RNA-seq

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Zhang, Z., Luo, D., Zhong, X., Choi, J. H., Ma, Y., Wang, S., Mahrt, E., Guo, W., Stawiski, E. W., Modrusan, Z., Seshagiri, S., Kapur, P., Hon, G. C., Brugarolas, J., & Wang, T. (2019). Scina: Semi-supervised analysis of single cells in silico. Genes, 10(7), [531]. https://doi.org/10.3390/genes10070531