Integrated Analysis of Long Noncoding RNA and Coding RNA Expression in Esophageal Squamous Cell Carcinoma
Figure 1
Transcriptomic landscape of esophageal squamous cell cancer (ESCC). (a) Whole transcriptome of tumor (T) and adjacent normal tissue (N) of four patients with ESCC were detected using a microarray with 7,419 long noncoding RNAs (lncRNAs) and 27,958 coding RNAs. Two main clusters (Ts and Ns) were generated using unsupervised clustering methods. Then, a self-organizing map (SOM) of either whole transcriptome (both lncRNAs and mRNAs) or lncRNAs or mRNA was produced from each sample (see legend in up-left corner of this figure, and the arrows are meant to indicate the potential interaction), using gene expression dynamic inspector (GEDI). Mosaic patterns are pseudocolored SOMs to show integrated biological entity in each sample. Red through blue color indicates high to low expression level. (b) and (c) Differentially expressed lncRNAs (DE-lncRNAs) and coding RNAs (DE-mRNAs) in ESCC. Hierarchical clustering analysis of 410 DE-lncRNAs (b) and 1219 DE-mRNAs (c) between ESCC tissue and adjacent normal tissue (fold change > or < 2-fold and ). Red and green colors indicate high and low expression, respectively. In the heatmap, columns represent samples, and rows represent each gene. The scale of expression level is shown on the horizontal bar. (d) KEGG functional analysis of DE-mRNA networks in ESCC. The DE-mRNA genes are involved in cancer-related signaling functions, and a detailed list of significant GO terms is shown in Figure S1 and its associated legend in Supplementary Information.
