To identify the possible target genes of the selected (Fig. 1D and E) differentially expressed lncRNAs via cis- or trans-regulatory effects, two previously described approaches were used36, 54. The genes transcribed within a 10 kb window upstream or downstream of lncRNAs were considered as cis-target genes36, 54. The second method was used to identify trans-targets and is based on mRNA and microRNA sequence complementarity with the query lncRNA. For mRNA interactions we used a pre-computed database that catalogs the predicted lncRNA–RNA interactions55, where the accessible regions of the query lncRNA and possible targets (mRNA/lncRNA) are extracted, the binding energies of pairs of sequences (target and query) around the seed matches are evaluated and the minimum interaction energy of the joint secondary structures is calculated55. The 500 predicted targets (mostly constituting repeated targets with different interaction sites) with the lowest minimum free energies under −20 kcal/mol were taken in consideration for downstream analysis. For lncRNA and microRNA interaction prediction it was used rna22, a method for identifying microRNA-binding sites and their corresponding heteroduplexes56. It were selected those microRNAs with a folding energy lower than −20 kcal/mol.