Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps

Camden Jansen, Ricardo N. Ramirez, Nicole C. El-Ali, David Gomez-Cabrero, Jesper Tegner, Matthias Merkenschlager, Ana Conesa, Ali Mortazavi

Research output: Contribution to journalArticlepeer-review

39 Scopus citations


Rapid advances in single-cell assays have outpaced methods for analysis of those data types. Different single-cell assays show extensive variation in sensitivity and signal to noise levels. In particular, scATAC-seq generates extremely sparse and noisy datasets. Existing methods developed to analyze this data require cells amenable to pseudo-time analysis or require datasets with drastically different cell-types. We describe a novel approach using self-organizing maps (SOM) to link scATAC-seq regions with scRNA-seq genes that overcomes these challenges and can generate draft regulatory networks. Our SOMatic package generates chromatin and gene expression SOMs separately and combines them using a linking function. We applied SOMatic on a mouse pre-B cell differentiation time-course using controlled Ikaros over-expression to recover gene ontology enrichments, identify motifs in genomic regions showing similar single-cell profiles, and generate a gene regulatory network that both recovers known interactions and predicts new Ikaros targets during the differentiation process. The ability of linked SOMs to detect emergent properties from multiple types of highly-dimensional genomic data with very different signal properties opens new avenues for integrative analysis of heterogeneous data.
Original languageEnglish (US)
Pages (from-to)e1006555
JournalPLoS computational biology
Issue number11
StatePublished - Nov 1 2019


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