SCENIC: single-cell regulatory network inference and clustering

[en] 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.

Disciplines :

Computer science
Biochemistry, biophysics & molecular biology

Author, co-author :

Aibar, Sara; Katholieke Universiteit Leuven - KUL > Department of Human Genetics

González-Blas, Carmen Bravo; Katholieke Universiteit Leuven - KUL > Department of Human Genetics

Moerman, Thomas; Katholieke Universiteit Leuven - KUL

Huynh-Thu, Vân Anh ; Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Algorith. des syst. en interaction avec le monde physique

Imrichova, Hana; Katholieke Universiteit Leuven - KUL > Department of Human Genetics

Hulselmans, Gert; Katholieke Universiteit Leuven - KUL > Department of Human Genetics

Rambow, Florian; Katholieke Universiteit Leuven - KUL > Department of Oncology

Marine, Jean-Christophe; Katholieke Universiteit Leuven - KUL > Department of Oncology

Geurts, Pierre ; Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Algorith. des syst. en interaction avec le monde physique

Aerts, Jan; Katholieke Universiteit Leuven - KUL

More authors (4 more)

Language :

English

Title :

SCENIC: single-cell regulatory network inference and clustering

Publication date :

09 October 2017

Journal title :

Nature Methods

ISSN :

1548-7091

eISSN :

1548-7105

Publisher :

Nature Publishing Group

Volume :

Pages :

1083–1086

Peer reviewed :

Peer Reviewed verified by ORBi

Available on ORBi :

since 17 November 2017

Statistics

Number of views

747 (13 by ULiège)

Number of downloads

3010 (21 by ULiège)

More statistics

Scopus citations^®

3072

Scopus citations^®
without self-citations

3045

OpenCitations

1968

OpenAlex citations

4347

See more details

publications

supporting

mentioning

contrasting

Smart Citations

Citing PublicationsSupportingMentioningContrasting

View Citations

See how this article has been cited at scite.ai

scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.

Bibliography

Linnarsson, S. & Teichmann, S.A. Genome Biol. 17, 97 (2016).
Wagner, A., Regev, A. & Yosef, N. Nat. Biotechnol. 34, 1145-1160 (2016).
Stegle, O., Teichmann, S.A. & Marioni, J.C. Nat. Rev. Genet. 16, 133-145 (2015).
Raj, A. & van Oudenaarden, A. Cell 135, 216-226 (2008).
Moignard, V. et al. Nat. Biotechnol. 33, 269-276 (2015).
Pina, C. et al. Cell Rep. 11, 1503-1510 (2015).
Guo, M., Wang, H., Potter, S.S., Whitsett, J.A. & Xu, Y. PLoS Comput. Biol. 11, e1004575 (2015).
Huynh-Thu, V.A., Irrthum, A., Wehenkel, L. & Geurts, P. PLoS One 5, e12776 (2010).
Zeisel, A. et al. Science 347, 1138-1142 (2015).
Kiselev, V.Y. et al. Nat. Methods 14, 483-486 (2017).
Lake, B.B. et al. Science 352, 1586-1590 (2016).
Darmanis, S. et al. Proc. Natl. Acad. Sci. USA 112, 7285-7290 (2015).
Tirosh, I. et al. Nature 539, 309-313 (2016).
Tirosh, I. et al. Science 352, 189-196 (2016).
Alizadeh, A.A. et al. Nat. Med. 21, 846-853 (2015).
Johnson, W.E., Li, C. & Rabinovic, A. Biostatistics 8, 118-127 (2007).
Ritchie, M.E. et al. Nucleic Acids Res. 43, e47 (2015).
Perotti, V. et al. Oncogene 35, 2862-2872 (2016).
Chang, C.-Y. et al. Nature 495, 98-102 (2013).
Denny, S.K. et al. Cell 166, 328-342 (2016).
Müller, M.R. & Rao, A. Nat. Rev. Immunol. 10, 645-656 (2010).
Regev, A. et al. bioRxiv Preprint at: http://www.biorxiv.org/content/ early/2017/05/08/121202 (2017).
Zaharia, M. et al. In Proc. of the 9th USENIX Conference on Networked Systems Design and Implementation 2-2 (USENIX Association, 2012).
Marbach, D. et al. Nat. Methods 9, 796-804 (2012).
Islam, S. et al. Nat. Methods 11, 163-166 (2014).
Crow, M., Paul, A., Ballouz, S., Huang, Z.J. & Gillis, J. Genome Biol. 17, 101 (2016).
Lun, A.T.L., McCarthy, D.J. & Marioni, J.C. F1000Res. 5, 2122 (2016).
Friedman, J.H. Ann. Stat. 29, 1189-1232 (2001).
Chen, T. & Guestrin, C. In Proc.of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining 785-794 (ACM, 2016).
Freund, Y. & Schapire, R.E. Jinko Chino Gakkaishi 14, 771-780 (1999).
S?awek, J. & Arodz, T. BMC Syst. Biol. 7, 106 (2013).
Dean, J. & Ghemawat, S. Commun. ACM 51, 107-113 (2008).
Aerts, S. et al. PLoS Biol. 8, e1000435 (2010).
Herrmann, C., Van de Sande, B., Potier, D. & Aerts, S. Nucleic Acids Res. 40, e114 (2012).
Janky, R. et al. PLoS Comput. Biol. 10, e1003731 (2014).
Krijthe, J. Rtsne: t-distributed stochastic neighbor embedding using Barnes-Hut implementation https://github.com/jkrijthe/Rtsne (2015).
Marques, S. et al. Science 352, 1326-1329 (2016).
Macosko, E.Z. et al. Cell 161, 1202-1214 (2015).
Durinck, S. et al. Bioinformatics 21, 3439-3440 (2005).
Warde-Farley, D. et al. Nucleic Acids Res. 38, W214-W220 (2010).
Leek, J. sva: Surrogate Variable Analysis. R package version 3.24.4 (2017).
Smyth, G. limma: Linear models for microarray data. (2015).
Forbes, S.A. et al. Nucleic Acids Res. 45, D777-D783 (2017).
Edgar, R., Domrachev, M. & Lash, A.E. Nucleic Acids Res. 30, 207-210 (2002).

Similar publications

Sorry the service is unavailable at the moment. Please try again later.

Name	Provider / Domaine	Expiration	Description
JSESSIONID	Oracle Corporation www.uliege.be	Session	General purpose platform session cookie, used by sites written in JSP. Usually used to maintain an anonymous user session by the server.
CookieScriptConsent	CookieScript .uliege.be	1 year	This cookie is used by Cookie-Script.com service to remember visitor cookie consent preferences. It is necessary for Cookie-Script.com cookie banner to work properly.

Name	Provider / Domaine	Expiration	Description
_pk_id	InnoCraft Ltd .uliege.be	1 year	Used to store a few details about the user such as the unique visitor ID
_pk_ses	InnoCraft Ltd .uliege.be	30 minutes	Short lived cookies used to temporarily store data for the visit
_pk_ref	InnoCraft Ltd .uliege.be	6 months	Used to store the attribution information, the referrer initially used to visit the website