PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions
Figure 3
PERT captures cell culture effects.
(A) Experimental setup for profiling genome-wide transcriptome expression of uncultured (day-0) and culture-derived (day-4) colony forming unit-monocytes (CFU-M) and megakaryocytes (MEGA). Lin-: lineage-depleted cells; TPO: thrombopoietin; SCF: stem cell factor; FLT3LG: fms-related tyrosine kinase 3 ligand. (B) Pearson's correlation comparison between day-0 and day-4 samples. (C) Plots of Gene Ontology enrichment analysis showing the enrichment scores of cell cycle phase genes, immune response genes, and inflammatory response genes by day-4 samples compared with day-0 samples. NES denotes the normalized enrichment score. P-values (P) were calculated using the hypergeometric test. (D) Pearson's correlation comparison between day-0 CFU-M, day-4 CFU-M, and perturbed day-0 CFU-M (or model predicted day-4 CFU-M) gene expression profiles. (E) Pearson's correlation comparison between day-0 megakaryocyte, day-4 megakaryocyte, and perturbed day-0 megakaryocyte (or model predicted day-4 megakaryocyte) gene expression profiles.