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GeneGini: Assessment via the Gini Coefficient of Reference "Housekeeping'' Genes and Diverse Human Transporter Expression Profiles
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Cellular and Clinical Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
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2018 (English)In: Cell Systems, ISSN 2405-4712, Vol. 6, no 2, p. 230-+Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Cell Press , 2018. Vol. 6, no 2, p. 230-+
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-225213DOI: 10.1016/j.cels.2018.01.003ISI: 000427421500012PubMedID: 29428416Scopus ID: 2-s2.0-85042802316OAI: oai:DiVA.org:kth-225213DiVA, id: diva2:1194573
Funder
Knut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20180403

Available from: 2018-04-03 Created: 2018-04-03 Last updated: 2018-04-11Bibliographically approved

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CiteExportLink to record
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