Discovering sparse transcription factor codes for cell states and state transitions during development.

ABSTRACT: Computational analysis of gene expression to determine both the sequence of lineage choices made by multipotent cells and to identify the genes influencing these decisions is challenging. Here we discover a pattern in the expression levels of a sparse subset of genes among cell types in B- and T-cell developmental lineages that correlates with developmental topologies. We develop a statistical framework using this pattern to simultaneously infer lineage transitions and the genes that determine these relationships. We use this technique to reconstruct the early hematopoietic and intestinal developmental trees. We extend this framework to analyze single-cell RNA-seq data from early human cortical development, inferring a neocortical-hindbrain split in early progenitor cells and the key genes

SUBMITTER: Furchtgott LA 

PROVIDER: S-EPMC5352226 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature