Is there a list of mouse housekeeping genes available to download?

Question

[Marigold77]

Hello everyone,

I have searched though BioStars and although many threads ask about list of housekeeping genes, no answer can be found. So I'm taking the liberty of asking again: in there a comprehensive list of housekeeping genes in mouse available to view or download?

Basically, I want to be aware of which genes are housekeeping genes when looking at my RNA-seq data, because I'm doing a very exploratory research qualitatively assessing potential interesting genes (guided by data from another experiment).

Any help appreciated,

Ola

[Marigold77]

thanks a lot!

Answer 1

[User 59]

No, because there is no good definition of a 'housekeeping gene'. In fact most commonly used 'housekeeping' genes vary wildly in expression based on tissue type etc.

Following references liberally lifted from: https://cofactorgenomics.com/6-changes-thatll-make-big-difference-rna-seq-part-3/ to illustrate the problem

• http://www.ncbi.nlm.nih.gov/pubmed/15680211
• http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609175/

The following reference may be of interest however for specific mouse targets: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000898

Answer 2

[Bidossessi Wilfried]

You can find in the database "Housekeeping Transcript Atlas" reliable lists of human and mouse housekeeping genes.

Link: http://www.housekeeping.unicamp.br.

These lists were produced using a large and high quality RNA-seq data set. You can also access from the platform cell specific reference genes for expression normalization.

• http://www.housekeeping.unicamp.br/?homePageMouse
• http://www.housekeeping.unicamp.br/?homePageHuman

Answer 3

[brianpenghe]

Now universal housekeeping genes across 17 tissues have been summarized by this paper and can be downloaded here

[ccfpwll]

Cool paper! The download link doesn't seem to work, can you help update it?

[Zongxu Zhang]

Here is an updated link for this file: https://github.com/brianpenghe/Matlab-genomics/blob/master/He_2020_ENCODE3_RNA/GeneLists/Bulk%20Cluster%20Ubiquitous.txt But please be careful, when studying my interest question on tumor immunology, I found some of the nominated candidates from my list are presented in the list (e.g. Zc3h11a). I'm not sure how Dr. He gets the ubiquitous clusters of genes. But I recommend checking it before use.