PKO cell gene expression patterns converge and diverge with rho⁰ MEFs.

<p>(A) Principal Components Analysis (PCA) of TM6, rho⁰, PKO-1, and PKO-6 MEFs (n = 3 biological replicates per line; 12 replicates total). Expression profiles for each sample were plotted for their PC1 and PC2 scores, providing primary and secondary sources of variance, respectively. Samples were color-coded based on cell type. (B) Rank-rank hypergeometric overlap (RRHO) maps of the log₂ fold-change expression profiles between PKO and rho⁰ MEFs with respect to TM6 MEFs. Color coding represents–log₁₀ transformed hypergeometric <i>P</i> values, with higher values indicating strength of overlapping enrichment between PKO and rho⁰ gene lists. (C) Venn diagram of differentially expressed genes (DEGs) between rho⁰ MEFs (left) and PKO clones (right) with respect to TM6 MEFs. DEGs were identified in each comparison using an absolute log₂ fold-change threshold above 0.5 and a false discovery rate (FDR) adjusted Wald <i>P</i> value below 0.01. Clusters indicate rho⁰ specific (cluster 1), PKO specific (cluster 3), and shared DEGs (cluster 2). (D) Dotplot of Gene Ontology (GO) overrepresentation analysis (ORA) of the rho⁰ specific, shared, and PKO specific DEG clusters. Dot size indicates the ratio of genes from the selected ontology set in the DEG cluster, color indicates significance of gene set overrepresentation in the cluster (FDR adjusted <i>P</i> value) following hypergeometric significance testing.