INSISTC: Incorporating Network Structure Information for Single-Cell Type Classification

Motivation Uncovering gene regulatory mechanisms in individual cells can provide insight into cell heterogeneity and function. Recent accumulated single-cell RNA sequencing data have made it possible to analyze gene regulation at single-cell resolution. On the other hand, understanding cell-type-specific gene regulation can also assist in more accurate cell type and state identification. Computational approaches utilizing gene regulatory relationships for single-cell type classification are under development. Methods pioneering in integrating gene regulatory mechanism discovery with cell-type classification encounter challenges such as how to accurately determine gene regulatory relation-ships and how to incorporate gene regulatory network structure into consideration. Results We developed a computational method to incorporate gene regulatory network structure information for single-cell type classification (INSISTC). INSISTC is capable of identifying cell-type-specific gene regulatory mechanisms while performing single cell type classification. Tested on three mouse scRNA-Seq datasets, including thousands of single-cell samples, INSISTC demonstrated its accuracy in cell type classification and its potential for providing insight into molecular mechanisms specific to individual cells. In comparison with the alternative methods, INSISTC demonstrated its complementary performance for gene regulation interpretation. Availability https://hulab.ucf.edu/research/projects/INSISTC/ Contact [email protected] or [email protected] Supplementary information Supplementary data are available at xxxxxx online.