I have got some differentially expressed (DE) lncRNA and DE coding genes from an RNA-seq analysis (human). Then, I did a co-expression analysis to get the co-expressed DE coding genes with DE lncRNA. As the RNA-seq data (CPM was used) was not normal, I used the Spearman correlation test. However, almost all coding genes showed the negative and the positive correlation with the various lncRNA. I did the GO and pathway analysis of coding genes that co-expressed with lncRNA to find the biological function of corresponding lncRNAs. But, as the coding gene list (for both negative and positive correlations) was almost the same, I could not obtain the distinct results for coding genes with the positive and negative correlation. For solving the issue, I tried to restrict the analysis to cis-lncRNAs, so I obtained the coding genes near the lncRNA (300 kbp, upstream and downstream), but these near coding genes showed both negative and positive correlation with various lncRNAs. Could you please kindly advise me in this regard?