sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network

Xu, Yang; Begoli, Edmon; McCord, Rachel Patton

doi:10.1038/s41540-022-00245-6

sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network

Journal Article · Mon Sep 12 00:00:00 EDT 2022 · npj Systems Biology and Applications

DOI:https://doi.org/10.1038/s41540-022-00245-6· OSTI ID:2469818

^[1]; Begoli, Edmon ^[2]; ^[1]

University of Tennessee, Knoxville, TN (United States)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); University of Tennessee, Knoxville, TN (United States)

The boom in single-cell technologies has brought a surge of high dimensional data that come from different sources and represent cellular systems from different views. With advances in these single-cell technologies, integrating single-cell data across modalities arises as a new computational challenge. Here, we present an adversarial approach, sciCAN, to integrate single-cell chromatin accessibility and gene expression data in an unsupervised manner. We benchmarked sciCAN with 5 existing methods in 5 scATAC-seq/scRNA-seq datasets, and we demonstrated that our method dealt with data integration with consistent performance across datasets and better balance of mutual transferring between modalities than the other 5 existing methods. We further applied sciCAN to 10X Multiome data and confirmed that the integrated representation preserves biological relationships within the hematopoietic hierarchy. Finally, we investigated CRISPR-perturbed single-cell K562 ATAC-seq and RNA-seq data to identify cells with related responses to different perturbations in these different modalities.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 2469818

Journal Information:: npj Systems Biology and Applications, Journal Name: npj Systems Biology and Applications Journal Issue: 1 Vol. 8; ISSN 2056-7189

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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