Entering edit mode
5.2 years ago
msimmer92
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300
Hello all. Is there some updated list of HUMAN housekeeping genes to use in analyses? Maybe someone already made a neat list somewhere readily available to be used by bioinformaticians.
I found https://www.tau.ac.il/~elieis/HKG/ but it´s based on a paper from 2013. I wanted to check if this is still good to use or if there´s an updated version (because it´s from 2013..).
Thank you.
What kind of analysis? Did you searched literature already?
I just want a list of housekeeping genes. I want to know if that one i found is the most updated one or not. Yes, I´ve searched and I´ve found that one, and it seems to be the best one since it´s mentioned in a lot of places, but it´s from 2013. So I want to check here, since I can reach a bigger amount of people with more experience.
it´s for quality control of RNA-seq data.
Thanks for adding the extra information.
You can find in the database "Housekeeping Transcript Atlas" up to date version of human and mouse housekeeping genes. http://www.housekeeping.unicamp.br.
Are human housekeeping genes likely to change over time? What do you think?
But methods, papers and experiments get updated all the time, or fine-tuned or even invalidated. For example, at first they used microarrays and then they did it with RNA-seq because technology changed. This might shield different results that might be slightly different or very. I think it´s a fair question, not from the biology point of view, and it´s good to continue double checking in the community, specially when the publication is 6 years old at this rapidly-changing time.
My question was meant to generate thought and was not to question validity of your original post.
If your only considerations is QC then would it matter that much if the list had a few more or less members. I have not seen people around me specifically check for certain genes in the manner you are planning to use them. At what point were you thinking of using this information for QC? After you create your normalized counts in DESeq2? And what would be your criteria to decide pass/fail bar for samples?
Ok, sorry, it is difficult to assess intention through here. Regarding your second question, yes, it is after normalized counts in DESeq2. We are thinking to use it as a check because it has happened in the lab that a person produced RNA-seq data and someone was analysing it for differential expression, and that person found out that a lot of genes that are vital for the cells weren´t being expressed, which made them think there may be a problem with the data. After that, some people in my lab started wanting to have some sort of checkup of that, to validate the data (that´s why I called it quality control). For that, they thought to get a list of housekeeping genes to make sure that, at least if they see something weird in their expression, they will be suspicious and run follow-up tests. They haven´t decide so far the criteria (how many housekeeping genes to use to declare a dataset "approved", and which ones) since it´s something new for them, and this is why we are revising this literature (any opinion on this regard is also welcome, by the way). That website I cited seems to have the answer, but because I saw 2013 I wanted to double check and I wrote this question here.
Have you looked to see how much overlap is there between genes that your lab considers vital for cells and the gene list you posted in original question. The purpose of posted list is clearly stated:
highly uniform and strongly expressed genes that may be used for experimental calibration, e.g. as PCR control genes.It sounds like your needs are of a qualitative nature so it may be worth looking at your internal data to see what the genes on the posted list look like. It may already give you upper/lower bounds to consider for QC purposes, while you wait for additional answers.
Just to add that, for a recent NanoString experiment, we had used:
Yes , I think this is the most reasonable thing to do. Thank you for your opinion! @genomax