Wu J, Li M & Zhang Y. Long noncoding RNA HOXA‐AS2 regulates the expression of SCN3A by sponging miR‐106a in breast cancer. Journal of Cellular Biochemistry (2019)

How they used Xena

These authors downloaded breast cancer data from Xena and then ran their analyses.

Paper

Long noncoding RNA HOXA‐AS2 regulates the expression of SCN3A by sponging miR‐106a in breast cancer.

Breast cancer is the most commonly diagnosed cancer that affects women worldwide. This study aimed to investigate the competing endogenous RNAs (ceRNAs) mechanism in breast cancer. Microarray data were downloaded from the University of California Santa Cruz (UCSC) Xena database. The limma package was used to screen the differentially expressed messenger RNAs (DEMs) and differentially expressed long noncoding RNAs (DELs). Subsequently, functional analysis was performed using DAVID tool. After constructing the protein‐protein interaction (PPI) network, we identified the major gene modules using the Cytoscape software. Univariate survival analysis in the survival package was performed. Finally, the ceRNA regulatory network was constructed to identify the critical genes. A total of 1380 DEMs and 345 DELs were identified in breast cancer samples compared with normal samples. Functional enrichment analysis showed that DEMs were mainly involved in cell division, and cell cycle. We screened four major gene modules and identified the hub nodes in these functional modules. Several DEMs (including FABP7, C4BPA, and LAMB3) and three long noncoding RNAs (lncRNAs) (LINC00092, SLC26A4.AS1, and COLCA1) exhibited significant correlation with patients’ survival outcomes. In the ceRNA network, the lncRNA HOXA‐AS2 regulated the expression level of SCN3A by interacting with hsa‐miR‐106a‐5p. Thus, our study investigated the ceRNA mechanism in breast cancer. The results showed that lncRNA HOXA‐AS2 might modulate the expression of SCN3A by sponging miR‐106a in breast cancer.