Hi there, I am currently analyzing the singling pathway with lncRNA2Function. But some of the lncRNAs can not be recognized by the datebase. It showed this message "The following lncRNAs that you input could not be found in the Ensembl v70 (GENCODE v15) and were excluded from the enrichment analysis". My concern is that whether the Ensembl Gene ID is different between the old Ensembl version and the current version. If it is, how can I convert the current version into the old version? Thanks!
Have you tried with Gene Symbols ? It might work effectively with that. Also try by removing revision numbers in the end of the gene name. Example 'ENSG00000228630' instead of 'ENSG00000228630.2'.
Since lncRNA2function study was based on Gencode v15, there is a possibility that it does not include the new lncRNAs. http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-16-S3-S2
The lncRNAs are increasing day by day and there is huge difference between v15 and current versions or the latest version based on hg19 (gencode v19). It means whatever RNAs lncRNA2function says does not match means, it was not there when they carried out the study. http://www.gencodegenes.org/releases/
Example: Number of lincRNA class in Gencode v15 is 6,458 and v19 is 7,114 ( other classes also have huge difference)
I could not also find any annotation update history from lncRNA2Function website. The predictions are still based on v15.