Fig. 1

Transcriptomic analysis of the nine CTC lines obtained from a patient with metastatic colon cancer at different times during disease progression. a Unsupervised 3D PCA representing the gene expression patterns of the CTC line obtained before treatment (n = 3 samples) and the eight CTC lines obtained after treatment initiation (n = 10 samples); b Hierarchical clustering of the CTC lines based on the differentially expressed transcripts (DETs) in CTC-MCC-41 (before treatment) and the other eight lines. The color intensity indicates the transcript expression level (red for upregulated transcripts and blue for downregulated transcripts); c Volcano plots showing the distribution of gene expression fold changes and p-values using the TAC software. Transcripts upregulated in CTC-MCC-41 are indicated in green, and transcripts upregulated in the other eight CTC lines are in red. d Top enriched pathways for the DETs (ANOVA analysis), ranked in increasing order (Fisher’s exact test p-value) identified by Ingenuity® Pathway Analysis, by comparing CTC-MCC-41 (before treatment) and the other eight lines. The “EIF2 signaling”, “mTOR and “PI3K/AKT signaling” pathways were significantly deregulated. Red: genes upregulated in CTC-MCC-41 compared with the other eight CTC lines; green: genes upregulated in the eight post-treatment CTC lines; white: no overlap with the data set; Orange - log (p-value); e Volcano plots showing the distribution of gene expression fold changes and p-values using the TAC software, with transcripts upregulated in the CTC-MCC-41.5 [ABFG] subgroup (green) and in the CTC-MCC-41.5 [CDE] subgroup (red). f Top enriched pathways for the DETs based on the ANOVA analysis, ranked in increasing order (Fisher’s exact test p-values) identified by Ingenuity® Pathway Analysis, in the comparison of the seven CTC-MCC-41.5 lines obtained just before the patient’s death. Many “metabolism” pathways were significantly deregulated, including “xenobiotic metabolism signaling”. Abbreviations: TAC, Transcriptome Analysis Console; DET, differentially expressed transcripts