Fig. 6

RAICPE identifies multiple gene expression states during B cell development. a A proposed gene regulatory circuit governing B-lymphopoiesis, adopted from (Salerno et al., 2015). The network consists of 10 transcription factors (TFs). Red arrows represent transcriptional activation and blue bar-headed arrows represent transcriptional inhibition. b Average linkage hierarchical clustering analysis of the gene expression data from all the RACIPE models using the Euclidean distance. Each column corresponds to a gene, and each row corresponds to a stable steady state. Four major gene states (clusters) are identified. c 2D probability density map of the RACIPE-predicted gene expression data projected on to the first two principal component axes. d The microarray expression profiling of different stages during B cell development (van Zelm et al., 2005) projected on to the same axes as shown in (c) (See Additional file 1: SI 1.10). e Comparison between experimental gene expression of various stages with in silico clusters. Blue dots and red dots represent the Z-scores of genes from the RACIPE models and experiments, respectively. Error bar for each blue dot represents standard deviation of the RACIPE-generated gene expression values. f Comparison between experimental gene expression fold-change from stage Pro-B to stage Pre-B-I with the computed fold-change by RACIPE