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Novel ‘housekeeping’ genes and an unusually heterogeneous distribution of transporter expression profiles in human tissues and cell lines, assessed using the Gini coefficient

View ORCID ProfileSteve O’Hagan, Marina Wright Muelas, Philip J. Day, Emma Lundberg, View ORCID ProfileDouglas B. Kell
doi: https://doi.org/10.1101/155697
Steve O’Hagan
1School of Chemistry, 131, Princess St, Manchester M1 7DN, UK.
2The Manchester Institute of Biotechnology, 131, Princess St, Manchester M1 7DN, UK.
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Marina Wright Muelas
1School of Chemistry, 131, Princess St, Manchester M1 7DN, UK.
2The Manchester Institute of Biotechnology, 131, Princess St, Manchester M1 7DN, UK.
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Philip J. Day
2The Manchester Institute of Biotechnology, 131, Princess St, Manchester M1 7DN, UK.
3Faculty of Biology, Medicine and Health, The University of Manchester M13 9PL, UK.
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Emma Lundberg
4Science for Life Laboratory, Royal Institute of Technology (KTH), SE-17121 Solna, Sweden.
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  • For correspondence: dbk@manchester.ac.uk emma.lundberg@scilifelab.se
Douglas B. Kell
1School of Chemistry, 131, Princess St, Manchester M1 7DN, UK.
2The Manchester Institute of Biotechnology, 131, Princess St, Manchester M1 7DN, UK.
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  • For correspondence: dbk@manchester.ac.uk emma.lundberg@scilifelab.se
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Abstract

We analyse two comprehensive transcriptome datasets from human tissues and human-derived cell lines in terms of the expression profiles of the SLC and ABC families of membrane transporters. The Gini index (coefficient) characterises inequalities of distributions, and is used in a novel way to describe the distribution of the expression of each transporter among the different tissues and cell lines. In many cases, transporters exhibit extremely high Gini coefficients, even when their supposed substrates might be expected to be available to all tissues, indicating a much higher degree of specialisation than is usually assumed. This is consistent with divergent evolution from a more restricted set of ancestors. Similar trends hold true for the expression profiles of transporters in different cell lines, suggesting that cell lines exhibit largely similar transport behaviour to that of tissues. By contrast, the Gini coefficients for ABC transporters tend to be larger in cell lines than in tissues, implying that some kind of a selection process has taken place. In particular, with some exceptions such as olfactory receptors and genes involved in keratin production, transporter genes are significantly more heterogeneously expressed than are most non-transporter genes. The Gini index also allows us to determine those transcripts with the most stable expression; these often differ significantly from the ‘housekeeping’ genes commonly used for normalisation in transcriptomics and qPCR studies. The lowest four in tissues are FAM32A, ABCB7, MRPL21 and PCBP1, while the lowest three in cell lines are SF3B2, NXF1 and RBM45. PCBP1 is both reasonably highly expressed and has a low Gini coefficient in both tissues and cell lines, and is an excellent novel housekeeping gene. Overall, our analyses provide novel opportunities for the normalisation of genome-wide expression profiling data.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 26, 2017.
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Novel ‘housekeeping’ genes and an unusually heterogeneous distribution of transporter expression profiles in human tissues and cell lines, assessed using the Gini coefficient
Steve O’Hagan, Marina Wright Muelas, Philip J. Day, Emma Lundberg, Douglas B. Kell
bioRxiv 155697; doi: https://doi.org/10.1101/155697
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Novel ‘housekeeping’ genes and an unusually heterogeneous distribution of transporter expression profiles in human tissues and cell lines, assessed using the Gini coefficient
Steve O’Hagan, Marina Wright Muelas, Philip J. Day, Emma Lundberg, Douglas B. Kell
bioRxiv 155697; doi: https://doi.org/10.1101/155697

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