Prediction of target genes and enrichment analysis

cis- or trans-acting algorithms were used to predict the potential targets of lncRNAs. The first algorithm predicted potential target genes of cis-acting lncRNAs that were physically located within 10 kb upstream or 20 kb downstream of lncRNAs using liftOver genome browser (genome.ucsc.edu/cgi-bin/hgLiftOver). The second algorithm predicted potential target genes of trans-acting lncRNAs based on the lncRNA-mRNA complementary sequences, and predicted lncRNA-mRNA duplex energy. First, BLASTN (29) was performed to detect potential target mRNA sequences with >95% identity and E value <1×10⁻⁵ (https://blast.ncbi.nlm.nih.gov/Blast.cgi). Then, RNAplex (30) was used to calculate the complementary energy between lncRNAs and their potential trans-regulated target genes with RNAplex-10⁻³⁰. Gene Ontology (GO) (31) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (32) enrichment analyses of the identified potential target genes were performed using the Database for Annotation, Visualization and Integrated Discovery (33); and P<0.05 was considered to indicate a statistically significant difference.