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Cell Syst. 2018 Feb 28;6(2):230-244.e1. doi: 10.1016/j.cels.2018.01.003. Epub 2018 Feb 7.

GeneGini: Assessment via the Gini Coefficient of Reference "Housekeeping" Genes and Diverse Human Transporter Expression Profiles.

Author information

1
School of Chemistry, 131, Princess Street, Manchester M1 7DN, UK; The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK.
2
The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK; Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
3
Science for Life Laboratory, Royal Institute of Technology (KTH), SE-17121 Solna, Sweden. Electronic address: emma.lundberg@scilifelab.se.
4
School of Chemistry, 131, Princess Street, Manchester M1 7DN, UK; The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK. Electronic address: dbk@manchester.ac.uk.

Abstract

The expression levels of SLC or ABC membrane transporter transcripts typically differ 100- to 10,000-fold between different tissues. The Gini coefficient characterizes such inequalities and here is used to describe the distribution of the expression of each transporter among different human tissues and cell lines. Many transporters exhibit extremely high Gini coefficients even for common substrates, indicating considerable specialization consistent with divergent evolution. The expression profiles of SLC transporters in different cell lines behave similarly, although Gini coefficients for ABC transporters tend to be larger in cell lines than in tissues, implying selection. Transporter genes are significantly more heterogeneously expressed than the members of most non-transporter gene classes. Transcripts with the stablest expression have a low Gini index and often differ significantly from the "housekeeping" genes commonly used for normalization in transcriptomics/qPCR studies. PCBP1 has a low Gini coefficient, is reasonably expressed, and is an excellent novel reference gene. The approach, referred to as GeneGini, provides rapid and simple characterization of expression-profile distributions and improved normalization of genome-wide expression-profiling data.

KEYWORDS:

Gini index; Human Protein Atlas; SLCs; cell atlas; drug transporters; housekeeping genes; tissue specificity; transcriptome

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