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[Arabidopsis] How many genes are transcribed?

M Marks via arab-gen%40net.bio.net (by marks004 from umn.edu)
Fri Apr 12 14:06:39 EST 2013


Hi Howie,

In the case of isolated trichomes from various genotypes (Marks et al.,
2009 Mol Plant 2: 803-822; Gilding and Marks 2010 Plant Journal
64:304-317), we could detect above background expression of 11,000 - 12,500
genes on average using the ATH1 chips. In this case, an above background
signals in multiple replicates was needed to make a detection call.  Still
many arrays gave low signals that could represent false positives, and some
genes may be functionally expressed at very low levels and would not be
called detected. In addition, leaky transcription of some genes without
functional significance may inflate the numbers.

David

On Tue, Apr 9, 2013 at 3:07 AM, howie newick <howie.newick from gmx.net> wrote:

>
>    Dear colleagues,
>    I was recently thinking about the active vs the inactive part of the
>    transcriptome. I would be very interested to get an idea of the
>    percentage of genes that is actually actively transcribed at any stage
>    of development. I could make an educated guess and speculate that
>    maybe 60-70% of the genes are being transcribed (on average), but has
>    this been ever quantified?
>    Although error-prone, one approach may be to look at microarray data
>    and use certain intensity cutoffs. But again, these cutoffs are
>    arbitrary ...
>
>    I would greatly appreciate ideas from the community.
>    Thank you very much in advance,
>
>    Howie
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-- 
M. David Marks
Professor
Department of Plant Biology
University of Minnesota

1445 Gortner Ave Rm 250
St. Paul, MN 55108

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