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Fig. 4 | Genome Biology

Fig. 4

From: Intergenic disease-associated regions are abundant in novel transcripts

Fig. 4

Identification of novel transcripts expressed in skin cutaneous melanoma. a of novel transcript types identified through CaptureSeq on 13 melanoma transcriptomes, targeting regions proximal to key melanoma genes. Red lines denote novel splice junctions, red blocks novel exons, and gray boxes the captured regions. From top to bottom: a fusion protein between GRM5 and NOX4, novel exons on ACAT1, novel lncRNAs bidirectional to ENSA, and an antisense lncRNAs overlapping ADAMTLS4. b, c Violin plot of fold change of novel transcripts in primary tumor and metastatic samples vs normal. Red dots denote significant differences (FDR < 0.01). Out of 31 novel transcripts, 22 were detectable in both TCGA primary tumors and metastatic samples. d Kaplan–Meier survival curve for captured transcript GCSM011 in metastatic melanomas. Red lines mark the groups in the upper half of transcript expression and blue for the lower half. e Schematic representation of genomic loci of GCSM011 between MCL1 and ENSA. f Allelic imbalance of captured transcripts in haploblocks associated with melanoma. Heterozygous sites were predicted with QuASAR [116] and allelic imbalance calculated with MBASED [117]. Y-axis represents median allelic expression across heterozygous SNPs. Allelic imbalance displayed as absolute value of 0.5 – allelic imbalance. Homozygous and heterozygous SNPs with allelic or without allelic imbalance are shown in blue, red, and yellow, respectively. At least 30 reads had to be observed over a SNP, with significance cutoff of FDR < 0.1

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