Where can I find list of housekeeping(HK) genes?

Question

[Natasha]

Hello,

I am looking for the list of housekeeping(HK) genes reported in a study

According to the supplementary data reported here ( sheet named : EST6909HK), there are 6910 HK genes. The number of HK genes appears to be quite large. Could someone look into the data presented in the above study ?

I am not sure if I have misinterpreted the information. Also, I would like to know if there are other studies that report the list of housekeeping genes in humans, particularly the studies that have considered liver, muscle, pancreas, kidney, brain, heart and blood in the list of tissue samples that have been used to arrive at the list of HK genes.

[lakhujanivijay]

Hi Natasha

"Housekeeping genes" is not a good title for this post. Please write informative and meaningful titles for your question. We have done it for you this time.

Answer 1

[JC]

The paper reports what the authors consider HK genes based on microarray and EST data. We have decades claiming that there is no concept of HK genes because, after RNA-seq technology revealed, the gene expression level of any gene is highly variable at the transcript level. In many experimental designs is much better to obtain your control genes directly for the data and not force your results to fit preselected genes.

Here are some further readings:

1. https://www.ncbi.nlm.nih.gov/pubmed/23810203
2. https://www.ncbi.nlm.nih.gov/pubmed/28242599

[johdgy]

In many experimental designs is much better to obtain your control genes directly for the data and not force your results to fit preselected genes.

how to obtain control genes directly, Can you please further explain it

[JC]

Many normalization methods don't preselect genes, for example, TMM algorithm in EdgeR looks for the more stable genes in your data.

Answer 2

[brianpenghe]

Here you can find a list of universal housekeeping genes across 17 tissues have been summarized by this paper and can be downloaded here

[Ram]

This paper is on mouse tissue. Does the data apply to mouse genes or human genes?

[brianpenghe]

The data are in mice. But by converting mouse genes to human orthologs using ENSEMBL biomart etc you can get a human list. Housekeeping genes are usually highly conserved so there shouldn't be a lot of differences between mouse and human.