Detection of Housekeeping genes

Question

[glady]

How can we detect housekeeping genes from a genome ? Is there any tool available freely online for this purpose ? Thank you in advance for your replies.

[GenoMax]

How can we detect housekeeping genes from a gene ?

As written the question does not make sense. Perhaps you meant to say genome?
Housekeeping genes have generally been those whose expression is not affected by the experimental condition being tested. They are not a completely foolproof in all experimental situations.

[glady]

Yes, it is *genome. Sorry for the mistake, I have edited my question.

[natasha.sernova]

The most obvious definition is present in WIKI.

https://en.wikipedia.org/wiki/Housekeeping_gene

Let's see, how to find them and if it is possible.

There are a few tools, as described here for example.

https://arxiv.org/ftp/arxiv/papers/1301/1301.3077.pdf

Kerfuffle: a web tool for multispecies gene colocalization analysis

and their rather old reference:

http://sci-hub.cc/10.1038/ng887#

Lercher MJ, Urrutia AO, Hurst LD: Clustering of housekeeping genes provides a unified model of gene order in the human genome . Nat Genet 2002, 31(2):180-183.

Usually the detection is done with RNA-analysis like described below:

http://physiolgenomics.physiology.org/content/21/3/389

GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues

This is sooner experimantal problem:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811673/

Application of housekeeping npcRNAs for quantitative expression analysis of human transcriptome by real-time PCR

Answer 1

[WouterDeCoster]

Since housekeeping genes are highly tissue-specific it's important to chose the right genes in the tissue of interest. I would also suggest to use more than one housekeeping gene in your experiment. A tool (only partially freely available) which collected a lot of microarray data is genevestigator which has information about the most appropriate housekeeping genes. Alternatively, RNA-seq data from your species and tissue of interest could be used to detect invariable genes, but you always need to validate that what you think is invariable, truly is invariable under the condition of interest by qPCR or similar.

[glady]

thank you for your reply, its really helpfull.

Answer 2

[brianpenghe]

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