Question about Co-expression analysis and finding targets for lncRNAs I have a dataset with 88 tumor and 113 normal samples. Among the 50k genes after filtering there are a total of 28k genes (both mRNAs and lncRNAs)

I wanted to do co-expression analysis between lncRNAs and mRNAs to find the targets for each lncRNA. I'm thinking to use WGCNA for co-expression network analysis.

Few doubts:

1) For Co-expression network analysis (WGCNA) should I use only tumor samples (or) both tumor and normal samples?

2) If not WGCNA, if I use cor function in R with method Pearson, on what cutoff I should select the target genes?

3) Heard that with bedtools we can know which genes are 10kb upstream/ downstream of lncRNAs to find neighboring pc genes. But no idea how to do that. Could you please give me an example for this.

Thank you
You have several options to approach this with WGCNA (weighted correlation network analysis). You can run a WGCNA on the combined set, identify modules and select those lncRNAs for further follow-up that have relatively high intra-modular connectivity (i.e., are intramodular hub genes). I would suggest this approach first.

Second option is to run WGCNA on mRNA for coding genes only and screen module eigengenes and lncRNAs for association with one another. This approach is usually helpful when the two data types (mRNA and lncRNAs) are different which I suppose is not really your case (mRNA and lncRNAs were probably measured together and are overall similar).  

I would start using all samples together (tumor and normal). Hopefully you'll find some interesting and plausible information; in the second pass I'd perhaps create separate (or consensus) networks for tumor and normal samples. 

I am not familiar with bedtools, but you should have some sort of gene/transcript annotation with your data (it was surely aligned to a reference genome and summarized to some sort of annotated set of genes). The annotation should contain chromosome and base pair position, which would make it rather easy to find genes within a specific interval.