Fig. 3
From: Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studies
Gene expression based classification of CRC cell lines revealed a separation between colon-like and undifferentiated cell lines associated with the consensus molecular subtypes (CMS). a PCA of cell line mRNA expression data (plotted as sample-wise PC1 versus PC2) showed that the cell lines had a bimodal density distribution along PC1 (bottom plot), indicating two distinct subgroups largely separating CMS2/3 from CMS1/4. Each point represents one cell line, and is colored according to the CMS class and with point type indicating MSI-status. Dashed vertical line (red) indicates the least frequent value between the two density modes of PC1, and was used as a threshold to separate the cell lines into the two subgroups. b PC1 (horizontal axis) was strongly correlated with the sample-wise enrichment score for a set of gastro-intestinal tissue enhanced genes (vertical axis), and cell lines with high enrichment scores, left of the red dashed line, were termed “colon-like” and the remaining “undifferentiated”. c Gene set enrichment analyses comparing colon-like and undifferentiated cell lines showed that colon-like cell lines had higher expression of genes upregulated by HNF4A and lower expression of genes related to colorectal cancer stemness. Undifferentiated cell lines had higher expression of genes related to epithelial to mesenchymal transition and genes upregulated by TGFβ. The plot includes the top 15 gene sets tested (ranked by p-value) and the -log10 p-value is plotted on the horizontal axis. d Top 5 differentially expressed transcription factors and kinases (mRNA level), miRNAs and proteins between colon-like and undifferentiated cell lines. mRNAs and miRNAs are ranked by p-value while proteins are ranked by absolute log2 fold-change. The log2 fold-changes (log2FC) between the sample groups are indicated. e Classification of the individual cell lines according to the colon-like and undifferentiated subgroups. CRC: colorectal cancer, CMS: consensus molecular subtypes, log2FC: log2 fold-change, MSI/MSS: microsatellite instable/stable, PCA: principal component analysis