Un-biased housekeeping gene panel selection for high-validity gene expression analysis

Ana I Casas*, Ahmed A Hassan, Quirin Manz, Christian Wiwie, Pamela Kleikers, Javier Egea, Manuela G López, Markus List, Jan Baumbach, Harald H H W Schmidt*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Differential gene expression normalised to a single housekeeping (HK) is used to identify disease mechanisms and therapeutic targets. HK gene selection is often arbitrary, potentially introducing systematic error and discordant results. Here we examine these risks in a disease model of brain hypoxia. We first identified the eight most frequently used HK genes through a systematic review. However, we observe that in both ex-vivo and in vivo, their expression levels varied considerably between conditions. When applying these genes to normalise expression levels of the validated stroke target gene, inducible Nox4, we obtained opposing results. As an alternative tool for unbiased HK gene selection, software tools exist but are limited to individual datasets lacking genome-wide search capability and user-friendly interfaces. We, therefore, developed the HouseKeepR algorithm to rapidly analyse multiple gene expression datasets in a disease-specific manner and rank HK gene candidates according to stability in an unbiased manner. Using a panel of de novo top-ranked HK genes for brain hypoxia, but not single genes, Nox4 induction was consistently reproduced. Thus, differential gene expression analysis is best normalised against a HK gene panel selected in an unbiased manner. HouseKeepR is the first user-friendly, bias-free, and broadly applicable tool to automatically propose suitable HK genes in a tissue- and disease-dependent manner.

Original languageEnglish
Article number12324
Number of pages12
JournalScientific Reports
Volume12
Issue number1
DOIs
Publication statusPublished - 19 Jul 2022

Keywords

  • Algorithms
  • Gene Expression
  • Gene Expression Profiling
  • Genes, Essential
  • Humans
  • Hypoxia, Brain
  • VALIDATION
  • IDENTIFICATION
  • REAL-TIME PCR
  • GEO
  • OMNIBUS
  • NOX4
  • NORMALIZATION
  • RNA-SEQ DATA
  • BRAIN
  • INAPPROPRIATE

Fingerprint

Dive into the research topics of 'Un-biased housekeeping gene panel selection for high-validity gene expression analysis'. Together they form a unique fingerprint.

Cite this