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Nat Methods. 2017 Nov;14(11):1083-1086. doi: 10.1038/nmeth.4463. Epub 2017 Oct 9.

SCENIC: single-cell regulatory network inference and clustering.

Author information

1
VIB Center for Brain & Disease Research, Laboratory of Computational Biology, Leuven, Belgium.
2
KU Leuven, Department of Human Genetics, Leuven, Belgium.
3
KU Leuven ESAT/STADIUS, VDA-lab, Leuven, Belgium.
4
IMEC Smart Applications and Innovation Services, Leuven, Belgium.
5
Department of Electrical Engineering and Computer Science, University of Liège, Liège, Belgium.
6
VIB Center for Cancer Biology, Laboratory for Molecular Cancer Biology, Leuven, Belgium.
7
KU Leuven, Department of Oncology, Leuven, Belgium.
8
KU Leuven, Department of Imaging and Pathology Translational Cell and Tissue Research, Leuven, Belgium.

Abstract

We present SCENIC, a computational method for simultaneous gene regulatory network reconstruction and cell-state identification from single-cell RNA-seq data (http://scenic.aertslab.org). On a compendium of single-cell data from tumors and brain, we demonstrate that cis-regulatory analysis can be exploited to guide the identification of transcription factors and cell states. SCENIC provides critical biological insights into the mechanisms driving cellular heterogeneity.

PMID:
28991892
PMCID:
PMC5937676
DOI:
10.1038/nmeth.4463
[Indexed for MEDLINE]
Free PMC Article

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