Question about retrogene track

[Katrin Rademacher]

hallo,

I have a question about the retrogene track and the labeling of retrogenes.  What is the difference between the expressed retrogenes from the ucscRetroExpressed5 table and the retrogenes from the ucscRetroInfo5 table, which are labelled with -2 (which stands for expressed retrogenes as well)?

If I download the ucscRetroExpressed5 table, there are also retrogenes inside labelled with 1 (stands for pseudogene).

Can you explain the difference to me?

Thanks in advance,

Katrin Rademacher

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Katrin Rademacher
M.Sc. Bioinformatics and Genome Research 
Institut für Humangenetik
Universitätsklinikum Essen
Hufelandstrasse 55
D-45122 Essen (Germany)
Tel: +49 (201) 723 4533
Fax: +49 (201) 723 5900
E-Mail: katrin.r...@uni-due.de

[Luvina Guruvadoo]

Hello Katrin,

Thank you for your question and our apologies for the delayed response. To answer your question, label = -2 in ucscRetroInfo5 are for expressed retros and label = 1 are not expressed or have weak evidence of expression. It should be noted that label field is pretty rough and it was decided later to add the "type" field to get a better idea of how much evidence there is for expression, so the label is not as useful and could be ignored.

I hope this helps. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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