Next Article in Journal
The FOXO’s Advantages of Being a Family: Considerations on Function and Evolution
Previous Article in Journal
Focusing on Adenosine Receptors as a Potential Targeted Therapy in Human Diseases
Previous Article in Special Issue
Computational Identification and Analysis of Ubiquinone-Binding Proteins
Open AccessArticle

Systematic Identification of Housekeeping Genes Possibly Used as References in Caenorhabditis elegans by Large-Scale Data Integration

1
College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
2
Scientific Research Office, Chongqing Normal University, Chongqing 401331, China
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Cells 2020, 9(3), 786; https://doi.org/10.3390/cells9030786 (registering DOI)
Received: 24 January 2020 / Revised: 11 March 2020 / Accepted: 11 March 2020 / Published: 24 March 2020
(This article belongs to the Special Issue Biocomputing and Synthetic Biology in Cells)
For accurate gene expression quantification, normalization of gene expression data against reliable reference genes is required. It is known that the expression levels of commonly used reference genes vary considerably under different experimental conditions, and therefore, their use for data normalization is limited. In this study, an unbiased identification of reference genes in Caenorhabditis elegans was performed based on 145 microarray datasets (2296 gene array samples) covering different developmental stages, different tissues, drug treatments, lifestyle, and various stresses. As a result, thirteen housekeeping genes (rps-23, rps-26, rps-27, rps-16, rps-2, rps-4, rps-17, rpl-24.1, rpl-27, rpl-33, rpl-36, rpl-35, and rpl-15) with enhanced stability were comprehensively identified by using six popular normalization algorithms and RankAggreg method. Functional enrichment analysis revealed that these genes were significantly overrepresented in GO terms or KEGG pathways related to ribosomes. Validation analysis using recently published datasets revealed that the expressions of newly identified candidate reference genes were more stable than the commonly used reference genes. Based on the results, we recommended using rpl-33 and rps-26 as the optimal reference genes for microarray and rps-2 and rps-4 for RNA-sequencing data validation. More importantly, the most stable rps-23 should be a promising reference gene for both data types. This study, for the first time, successfully displays a large-scale microarray data driven genome-wide identification of stable reference genes for normalizing gene expression data and provides a potential guideline on the selection of universal internal reference genes in C. elegans, for quantitative gene expression analysis. View Full-Text
Keywords: microarray; housekeeping gene; reference gene; Caenorhabditis elegans; RankAggreg microarray; housekeeping gene; reference gene; Caenorhabditis elegans; RankAggreg
Show Figures

Figure 1

MDPI and ACS Style

Tao, J.; Hao, Y.; Li, X.; Yin, H.; Nie, X.; Zhang, J.; Xu, B.; Chen, Q.; Li, B. Systematic Identification of Housekeeping Genes Possibly Used as References in Caenorhabditis elegans by Large-Scale Data Integration. Cells 2020, 9, 786.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop