Is there any straightforward way to identify housekeeping genes based on a series of genome-wide gene expression profiles? Literature searches suggest that meta-analysis of large-scale expression data can do the task, but what if the organism doesn't have enough expression data to mine? Is it safe to grab the genes with fold changes bouncing around one (0.9~1.1 range) if comparing all samples pairwise?
•
written
by
Vitis
2 answers
Yes, as you suggest using meta-analysis of microarray data can lead to good candidate for housekeeping genes on the basis of expression level stability across time and tissues. You should be able to extend a set of predicted housekeeping genes based on this approach from a species with abundant data to another related species without much microarray data, by finding the orthologs of candidate housekeeping genes. Proof of principle that this approach should work can be found in de Jonge et al (2007) "Evidence Based Selection of Housekeeping Genes", who perform microarray meta-analysis independently in human and mouse and show that:
...novel candidate housekeeping genes identified in the human data set also showed stability in expression in mouse arrays...
HTH, Casey
Depending on your species, finding orthologs may already have been done. Perhaps you should look for other posts on BioStar related to this issue.
Hi . You can find in the database HT Atlas reliable lists of human and mouse housekeeping genes. http://www.housekeeping.unicamp.br.
Log in to answer this question.
-
Herald: The Biostar Herald for Monday, January 22, 2024
written by Biostar
-
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
written by Julia Ma •
-
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
written by Novogene •
-
Blog: Next generation sequencing and its clinical applications
written by Novogene •
-
Differential expression analysis on multiple integrated datasets
written by michael.s •
-
Blog: Using RNA-seq to understand plants and improve crop yield
written by Novogene •
-
Forum: R - A bioinformatic analysis programming language for NGS
written by Novogene •
-
Job: Bioinformatics Research Consultant needed for constructing TFBS and regulatory networks from t…
written by tfhahn •
-
Gene expression meta-analysis: How to correctly compile a data set.
written by Tom •
-
Cross-species RNA-Seq analysis using edgeR with multiple factors?
written by dan.shea •
I think this answer depends on why you need to know the housekeeping genes. What is the plan for using them once you have them?
The main purpose is to identify a set of housekeeping genes to help normalize mRNA-Seq expression profiles across tissues and experiments. Much like what TMM normalization does, we'd like to use a set of housekeeping genes to calibrate or accommodate the RNA composition and/or sequencing depth difference across samples.