Constructing local cell-specific networks from single-cell data.

ABSTRACT: Gene coexpression networks yield critical insights into biological processes, and single-cell RNA sequencing provides an opportunity to target inquiries at the cellular level. However, due to the sparsity and heterogeneity of transcript counts, it is challenging to construct accurate gene networks. We develop an approach, locCSN, that estimates cell-specific networks (CSNs) for each cell, preserving information about cellular heterogeneity that is lost with other approaches. LocCSN is based on a nonparametric investigation of the joint distribution of gene expression; hence it can readily detect nonlinear correlations, and it is more robust to distributional challenges. Although individual CSNs are estimated with considerable noise, average CSNs provide stable estimates of networks, which

SUBMITTER: Wang X 

PROVIDER: S-EPMC8713783 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature