Analysis of gene expression microarray data of CD-1 versus C57BL/6J mice injected with drug revealed different pattern of lncRNAs.
Interesting experiment! But do not know the answer to your question...
Your heading is not clear. Do you mean where you can advertise your work? If so, you can just make a google search...
Thank you, I am looking for chromosome location of our mice lncRNA on human chromosomes. Or any method to do it.
The easiest way is to use liftover (file available to download from ucsc). The only thing you need to take care is that your region is not on the edge of a syntenic block. The easiest way to check is to liftover both ends of the region and the middle, and make sure that
1) all three are in the correct order
2) the distances are in line with what you would expect.
After that, you can do a local alignment and check if the sequence is correct on human.
lncRNAs are tricky to predict, and are often not conserved across human-mouse. You might check the promotor regions around the tss, or exon boundaries. But generally, in the individual case, it is a really pain to prove that the human gene is real or not / present or dead etc.
Here you have a pretty comprehensive list of conservation of lncRNAs across evolution.
Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.
http://www.ncbi.nlm.nih.gov/pubmed/25959816
You could use this as reference. As the other Leo suggested, liftoverables would be the best way to look for conservation. I would bin regions with highest liftoverables and rank accordingly. Additionally, i will overlay human EST data sets over this to see if there are any indication of transcription from the identified regions in humans. Then you can rank the conservation combining these two criteria for better reliability.
Keep an eye on pseudogenes and retrogenes which might obscure ur conservation data.
Hope this helps
Leo
Thank you, Leo. We did develop few algorithms which brought us multiple hits.
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