Question: What proportion of the (coding) genome is actually expressed at any given time?
0
gravatar for Dunois
6 weeks ago by
Dunois500
Dunois500 wrote:

(Please forgive me if this is a trivial/stupid question.)

Say a genome has n genes that code for proteins. Sampling the mRNA pool produced by this genome at time t yields m distinct mRNAs.

My question is, are there any estimates for what m/n is in general. (Like 5%, 50%, etc.) That is, what fraction of the genome (that codes for genes) is expressed at any give arbitrary time point?

If I were to pose this question a bit differently: say I have RNA-seq reads for an organism with a fully sequenced genome. What is the "typical" (?) mapping rate I should expect if I were to have the reads mapped to the genome (or to its CDS subset)?

ADD COMMENTlink modified 6 weeks ago by GenoMax96k • written 6 weeks ago by Dunois500
2
gravatar for Mensur Dlakic
6 weeks ago by
Mensur Dlakic9.1k
USA
Mensur Dlakic9.1k wrote:

It depends on the exact organism, genome size, tissue sample, developmental stage(s), day-night cycle and many other things. Larger number of genes are expressed in liver than brain. Larger proportion of genome is expressed in micro-organisms with reduced genomes than in salamanders. Impossible to answer globally without knowing more details about your experiment, and may be possible only in general terms even with that information.

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Mensur Dlakic9.1k
0
gravatar for GenoMax
6 weeks ago by
GenoMax96k
United States
GenoMax96k wrote:

What is the "typical" (?) mapping rate I should expect if I were to have the reads mapped to the genome (or to its CDS subset)?

While you will not likely see 100% mapping, a large fraction of reads should map to the genome you expect to see (anywhere from 70% upwards). Quality of the libraries will directly impact this number.

ADD COMMENTlink written 6 weeks ago by GenoMax96k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1268 users visited in the last hour
_