Integrated Analysis of Long Noncoding RNA and Coding RNA Expression in Esophageal Squamous Cell Carcinoma
Figure 3
Identification of lncRNAs co-located and co-expressed neighboring genes in esophageal squamous cell carcinoma (ESCC). (a) Identification of neighboring genes of the DE-lncRNAs. The genomic coordinate information of 410 DE-lncRNAs was used to search neighboring genes whose genomic locations are within ~5 kb upstream and ~1 kb downstream of the lncRNA and may extend to 1000 kb in both directions using GREAT software (http://bejerano.stanford.edu/great/public/html/index.php). The percentage of DE-lncRNAs harboring zero, one, or two neighboring genes is presented. (b) Gene Ontology (GO) enrichment analysis of lncRNAs co-located genes. Identified gene enriched pathways/terms are listed on the left; the length of horizontal bars and the numbers on the right indicate the percentage of genes involved in each pathway/term. (c) LncRNAs co-located and co-expressed coding mRNAs. Overlap of 538 DE-lncRNA co-located genes with 3307 DE-mRNAs in microarrays identified 76 lncRNAs co-located and co-expressed coding mRNAs (list in Table 2). GO enrichment analysis suggests phospholipase D1 (PLD1) and lysophosphatidylcholine acyltransferase1 (LPCAT1) are involved in ether lipid metabolism pathway. Genomic location shows that PLD1 is located at −22,068 bp upstream of ESCCAL-337 lncRNA on Chr 3 and LPCAT1 is at −21,250 bp upstream of ESCCAL-356 lncRNA on Chr 5.
