Hello,
I want to study the differentially expressed genes of Asian, African and European people.
Any ideas of which database I can download?
Thanks in advance for any help!
Best,
Yue
I think you are going to find it difficult to find an appropriate dataset. Well defined genetic populations are notoriously difficult to identify. Geographic (country of origin) and phenotypic (i.e. skin colour) are generally not good proxies for genetic population. I would refer you to recent tweet threads by Ewan Birney (head for the European Bioinformatics Institute). For example This, This, or This.
Even if you could identify coherent genetic groups, you would need to find a single study that contained data from multiple populations, because if you took two data sets, one from each population, you are likely to find that the batch effects between the studies are much bigger than the genuine differences between population.
If you look at some of the bigger RNA-seq collections a good population geneticist might be able to use the SNP calls to derive populations which you could then compare, but it won't be easy.
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Race is a terminology which is inappropriate and incorrect for humans.
May I inquire about the background to this study? - there are no statistically significant differences between the 'healthy' transcriptomes of these three groups - we are all the same species. If you conducted an experiment, and depending on the tissue of study, any differences that you find would be due to other factors, such as disparities in accessing healthcare, geographical considerations, dietary considerations, etc. There are of course known genetic polymorphisms that have higher or lower frequencies in each group, however, these do not translate into statistically significant differences at the gene expression level.
Before you draw conclusions from such a comparison, please keep in mind that intra-group variance is very likely to dwarf inter-group differences.
May I add that the terms "black" and "white" are offensive in most parts of the World. You start with Asian, why not follow with African and European thereafter?
Is "black" == "African" and "white" == "European"? How does OP define Asian? Is it South Asian, East Asian, Middle East, Northern Asia (Russia) or a combination of all the above? This stratification by continent makes no sense for a continent as vast and diverse as Asia.
You are absolutely right RamRS, and actually most genetic diversity between peoples is found in Africa. Probably because the origin of mankind is there. My point was more a political correct one, in most Western countries it is offensive to call peoples by their skin color, therefore also people here on Biostars might feel offended too. That was my point.
I agree with that point, of course. OP's categories are weird in that using them will result in exactly what Devon describes, where intra-group variance will dwarf any true inter-group differences.
I don't know, this topic is just really confusing as the categories are not mutually exclusive.