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Fig. 6 | Genome Biology

Fig. 6

From: Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci

Fig. 6

pcRNAs are differentially expressed in cancer. a Spearman’s rank-order correlation heatmap between tapRNAs and their associated coding genes in TCGA RNA-Seq V2 level 3 data. The correlation was calculated between the two matrices of TCGA RNA-Seq fold changes (Additional file 2: Figure S18a, b) and shows that the expression of pcRNAs and corresponding coding genes is correlated within specific cancers. b Spearman correlation between the expression of FOXA2 and FOXA2-DS-S in lung cancers (GSE18842 dataset). Tumour and normal individual samples are represented as blue and red dots, respectively. Boxplots on the right show that both transcripts are down-regulated in tumour compared to normal samples (Student’s t-test p values are indicated). c Invasion and migration assay analysis of Huh7 (left) and A549 (right) cells upon knock-down of FOXA2-DS-S using two different siRNAs (si1 and si2) compared to negative control siRNA. The bars show the mean of three biological replicate experiments. The error bars indicate the standard error of the mean. d Mutational analysis of CTCF and ZNF263 motifs associated with tapRNA loci. CTCF and ZNF263 motifs inside of tapRNA loci have significantly higher chances to be mutated in cancer. In total, we catalogued 241 CTCF motif mutations in 171 motif sites (37 cancer types) and 196 ZNF263 motif mutations in 135 motif sites (27 cancer types). e Example of a mutational analysis of CTCF and ZNF263 motifs associated within the ZEB2/ZEB2-AS/BT tapRNA locus, depicting the mutations found in melanomas. f Expression profile of ZEB2 and ZEB2-AS/BT in different cancers, showing concordant increased expression in malignancies, including skin cutaneous melanoma (SKCM)

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