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.
•
written
by
glady
2 answers
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.
Universal housekeeping genes across 17 tissues have been summarized by this paper and can be downloaded here
Log in to answer this question.
-
Extract Ribosomal DNA from Whole Genome Data
written by hafiz.talhamalik
-
Consensus sequence from SAM or BAM file?
written by lokraj2003
-
Extract Mitochondrial Genome Sequence from 1000 Genomes Data
written by ammarsabir15
-
Functional genes from meta-genomes
written by glady
-
Detection of CNVs from vcf file
written by misbahabas •
-
Highly Variable SNP
written by Sebastian •
-
Multiple genome alignment
written by glady
-
house keeping genes
written by glady
-
Human gut metagenome data
written by glady
-
generation of miRNA and gene networks
written by itsmeandleebzahra •
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.
Yes, it is *genome. Sorry for the mistake, I have edited my question.
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