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1h
revised Are there genes in sex chromosomes that determine facial features?
added 118 characters in body
1h
comment Are there genes in sex chromosomes that determine facial features?
Thanks anongoodnurse, done, and will do in future.
1h
comment Are there genes in sex chromosomes that determine facial features?
For which claim? Most of that is pretty basic. For the association with T and male facial characteristics see e.g. this
1h
answered Are there genes in sex chromosomes that determine facial features?
8h
comment Assuming if height was fully determined genetically, what would be the concordance between monozygotic pairs?
Yes, it would imply that the trait is almost completely determined by additive genetics. If you assume identical twins are as similiar in their environment as dizygotic twins (which twin studies do), then environmental factors like nutrition should be controlled for, and there are simple models you can use to account for sample size. There are a LOT of caveats to all this though, it's a complex field. There are good recommendations for books on population genetics on this forum that i recommend you pick up, if you want to do this kind of analysis.
8h
comment TRANSFAC Matrix.dat retrieve count matrix using BA or CC field
The basic method you're using is as good as any other simple model, and you won't do much better unless you want to invest a LOT more effort and do deep learning. The problem is that you can't pick any single 'most powerful' method because the threshold you pick will depend on the biological question you want answered. Also, be aware of what an approximation the PWM models are - you either have ChIP training data,which is v. messy, or PBM data, which doesn't reflect cellular conditions.
1d
comment TRANSFAC Matrix.dat retrieve count matrix using BA or CC field
That seems reasonable enough. The paper you cite is a little out of date, and I'd recommend reading some more recent ones as well. And be aware that if you use their threshold selection method you're going to get rather different results than the p-value based thresholds used in most papers.
1d
comment Which are the last cells of the human body to die?
When you say 'vital' do you mean - 'hard to kill'? The most 'vital' cells in the usual sense of the word - 'important for life' - are probably heart muscle, nerve cells etc, and these are exactly the ones that will die first because they use so much energy.
1d
answered Assuming if height was fully determined genetically, what would be the concordance between monozygotic pairs?
1d
comment TRANSFAC Matrix.dat retrieve count matrix using BA or CC field
Yes, unfortunately you clearly don't have the raw count matrix. The only other process which could have generated matrices like that is the process of adding pseudo counts. People often add things like (sqrt(BA)) before conversion to a PWM to avoid taking the log of zero. You could see if you can work out the original BA from that. In general though I'd avoid trying to recover bad data like that. Count matrices should be integers.
1d
awarded  Citizen Patrol
1d
comment TRANSFAC Matrix.dat retrieve count matrix using BA or CC field
Ah, sorry, my mistake. I didn't look at your numbers carefully enough. it looks like either those are already PWMs as opposed to count matrices (i.e. the values are log(count_freq/background_freq) ) or somebody has already done something strange to them. If it's the former you should have noticed some negative values. If it's latter you can try and do something like making the BA 100 and rounding them. Also it's not clear what algorithm you're talking about regularizing in that comment. Link?
2d
answered iPSC in drug discovery
2d
answered TRANSFAC Matrix.dat retrieve count matrix using BA or CC field
2d
awarded  Commentator
2d
comment Swapping genes?
+1 as I agree in general - but the specific example of the non coding genome being thought of as junk I think is wrong. We've known there was a lot of noncoding regulatory DNA since at least the late 90s. And the ENCODE project's 'it's all functional' line was just marketing.
2d
awarded  Yearling
2d
answered Genetic mutations and new alleles
Apr
30
answered What is a “homologous pair” of chromosomes in cross joining or cross over?
Apr
29
revised What makes DNA sequences most different/recognizable from a biological perspective?
added 54 characters in body