I am a little clueless when it comes to bioinformatics, but I need help please with understanding how to convert "XLOC" gene IDs of lncRNAs listed on an excel file (I downloaded it as a supplementary data file from a published article) to actual gene names. I do not have the original data all I have is the excel sheet with a column containing the list of lncRNAs in XLOC. detailed information would be highly appreciated.
XLOC_xxxxxx was the default transcript identifier created by the tool Cufflinks I believe. Cufflinks was used to create transcripts from RNA-seq reads aligned to the genome.
Each Cufflinks run created these identifiers for each BAM file analyzed. So it is not a systematic naming system, but was tied solely to that analysis of that bam.
So you need the associated data from the paper, and or to contact the original authors, and or to use the coordinates associated with that XLOC ID to get the sequence from that genome (if available).
In short, it is not a good choice to leave identifiers as default from a popular tool and publish it, because there will be many conflicting XLOC ids across the world.
LNCipedia is the best site to look for long non-coding RNA.
Following links inside brackets will take you to the page containing information about your XLOC_XXXXXs.
