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Fig. 5 | Genome Biology

Fig. 5

From: Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer

Fig. 5

Quantification of Iso-seq transcriptome in TCGA gastric cancer dataset. a T-sne plot of promoter activity in 315 TCGA gastric cancer samples (282 tumors and 33 normal). b Gene ontology analysis of the upregulated promoters in TCGA GC dataset. p value has been adjusted for gene length bias. c Volcano plot showing the log fold change in promoter activity in tumor samples. Novel promoters of several gastric cancer oncogene (FGFR4, MET, and ERBB3) are upregulated in the TCGA dataset (right). In an independent dataset (20 T-N pairs), novel promoters of MET and FGFR4 are also found to be upregulated while novel promoter for ERBB3 is not significantly upregulated. d Altered CDs by promoter activity status. Upregulated promoters have larger CD alteration. e Upper panel shows the gene isoforms initiated from the known and novel promoters of FGFR4, MET, and ERBB3. Lower panel shows the promoter activity and detection frequency in normal samples and TCGA subtypes of gastric cancer. Novel promoters are expressed at a lower level, but exhibited higher upregulation and are expressed in more tumor samples compared to normal samples. f Upper panel shows the protein domains of isoforms initiated from the known and novel promoters of FGFR4, MET, and ERBB3. Lower panel shows the signal peptide prediction in transcripts initiated from known and novel promoter sites, showing loss of signal peptide sequences in the novel isoforms

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