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  • 0 posts edited
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8h
comment Are there genes in sex chromosomes that determine facial features?
Thanks anongoodnurse, done, and will do in future.
9h
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
16h
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.
16h
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 The paper you cite is a little out of date, and I'd recommend reading some more recent ones as well.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
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.
2d
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
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.
Apr
28
comment Does a woman contain all the genes needed to make a man?
Also worth noting the existence of pseudoautosomal regions - "the genes other than SRY on the Y chromosome" are not all unique to men.
Apr
27
comment What did cyanobacteria gain from photosynthesis?
ATP is found in all known organisms, so there's every reason to think it would have been. Bacteria don't have mitochondria, so no, it wouldn't have been mitochondrial.
Apr
27
comment What did cyanobacteria gain from photosynthesis?
Literally everything an organism does requires energy. Photosynthesis provides an electrochemical gradient that can be used to make ATP - which is then used in many, many chemical reactions throughout the cell as an energy source. DNA synthesis requires ATP. RNA synthesis requires ATP. Protein synthesis requires ATP.
Apr
27
comment CRISPR/Cas for editing the human genome
It is true in general yes. But not in every case.
Apr
27
comment CRISPR/Cas for editing the human genome
"thousands similar to our target sites" is not true of all sites. It's true only of sites resembling repeats. Most sites in the genome can, for instance, have specific PCR primers designed against them. This would not be true if they all resembled repeats.
Apr
27
comment How significant is the genetic component of homosexual behaviour?
Be careful about the term 'environment' in these studies. In the breeders equation, which is the model used in most twin studies, "Non-shared environment" is just a miscellaneous bin used to account for all the variance not explained by the other terms. It therefore includes measurement error, developmental noise, etc etc. So even if environment as we usually think of it plays zero role, and it's all chance events during embryonic development, 'non-shared environment' will suck up that variance.
Apr
27
comment How significant is the genetic component of homosexual behaviour?
There is a 'genetic component' to homosexual behavior in that genes do predict it to some extent. They don't determine it though. As usual it's an interaction between many factors, most of which we don't understand.
Apr
20
comment Hardy-Weinberg equilibrium generalized to add inbreeding (non-random mating)
Yes, but these models are just simple approximations. Concepts like time and coalescence don't even exist the perfect binomial world of Hardy Weinberg :)
Dec
13
comment Does neural network in brain form cycles?
@CDB - true, fixed