Gencode v.15 annotation of the total differentially expressed lncRNAs in IBD and microarray validation by qPCR. (A) The Gencode v.15 array targeted 22,007 lncRNA transcripts falling into seven major annotation classes (antisense, processed transcripts, intergenic (lincRNAs), sense overlapping, sense intronic and retained introns). Three classes (ambiguous_orf, non-coding RNAs and TEC (to be experimentally confirmed) with small number of lncRNAs were merged into a miscellaneous (misc) class for better representation. (B) Three major classes of differentially expressed lncRNAs identified in our study: intergenic (lincRNAs), processed transcripts and antisense lncRNAs. (C) Differences between the expression levels of the top three most up- and down-regulated protein-coding genes (in blue) and lncRNA genes (in red) were tested using Kruskal-Wallis test with Dunn’s multiple comparison test. The top three up-regulated protein-coding genes (DUOXA2, CHI3L1 and CXCL9) and lncRNA genes (MMP12, FAM66D and SAA2-SAA4) showed increasing signal intensity from control group to inflamed CD and UC groups based on averaged gene expression levels (P-value <0.001). The top three down-regulated protein-coding genes (PCK1, GUCA2B and TNNC2) and lncRNA genes (DPP10-AS1, PDZK1P2 and ANRIL) showed decreasing signal intensity across the clinical subgroups from iCD and iUC to controls (P-value <0.001). (D) A total of eight genes were selected for real-time PCR validation of the microarray data in iCD versus control (red) and iUC versus control (blue). The log2 fold change is plotted on the y axis.