CLARIFY: cell-cell interaction and gene regulatory network refinement from spatially resolved transcriptomics.

ABSTRACT:

Motivation

Gene regulatory networks (GRNs) in a cell provide the tight feedback needed to synchronize cell actions. However, genes in a cell also take input from, and provide signals to other neighboring cells. These cell-cell interactions (CCIs) and the GRNs deeply influence each other. Many computational methods have been developed for GRN inference in cells. More recently, methods were proposed to infer CCIs using single cell gene expression data with or without cell spatial location information. However, in reality, the two processes do not exist in isolation and are subject to spatial constraints. Despite this rationale, no methods currently exist to infer GRNs and CCIs using the same model.

Results

We propose CLARIFY, a tool that takes GRNs as input, uses them and spat

SUBMITTER: Bafna M 

PROVIDER: S-EPMC10311313 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature