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Analysis and Meta-analysis of Transcriptional Profiling in Human Epidermis

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Epidermal Cells

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1195))

Abstract

Because of its accessibility, skin has been among the first organs analyzed using DNA microarrays; psoriasis, melanomas, carcinomas, chronic wounds, and responses of epidermal keratinocytes in culture have been intensely investigated. Skin has everything: stem cells, differentiation, signaling, inflammation, hereditary diseases, etc. Here we provide step-by-step instructions for bioinformatics analysis of transcriptional profiling of skin. We also present methods for meta-analysis of transcription profiles from multiple contributors, available in public data repositories. Specifically, we describe the use of GCOS and RMAExpress programs for initial normalization and selection of differentially expressed genes and RankProd for meta-analysis of multiple related studies. We also describe DAVID and Lists2Networks programs for annotation of genes, and for statistically relevant identification of over- and underrepresented functional and biological categories in identified gene sets, as well as oPOSSUM for analysis of transcription factor binding sites in the promoter regions of gene sets. This work can serve as a primer for researchers embarking on skinomics, the comprehensive analysis of transcriptional changes in skin.

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Notes

  1. 1.

    Increases you computer’s memory dedicated for this task.

  2. 2.

    Indicates to the program that chips 1–12; 25–30 and 42–66 belong to class 1, while 13–24, 31–41, and 67–68 belong to class 2 (controls) and that there are six sets of replicate chips.

  3. 3.

    Marks the leftmost column as containing the IDs of the genes.

  4. 4.

    Indicates to the program that there are three experiments with 24, 17, and 26 chips respecitvely.

  5. 5.

    Starts the program running (with 100 random permutations to derive p-values).

  6. 6.

    Plots a graph of regulated genes as shown in Fig. 9.

  7. 7.

    Exports the results of the analysis into a txt file with top 1,000 up- and downregulated genes

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Author information

Authors and Affiliations

  1. The RO Perelman Department of Dermatology, Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, NYU Cancer Institute, 455 First Avenue, New York, NY, 10016, USA

    Claudia Mimoso, Ding-Dar Lee & Miroslav Blumenberg

  2. Department of Dermatology, Faculty of Medicine, Taipei Veterans General Hospital, National Yang-Ming University, Taipei, Taiwan

    Ding-Dar Lee

  3. Mechanisms of Carcinogenesis Section, International Agency for Research on Cancer, Lyon Cedex, France

    Jiri Zavadil

  4. Wound Healing and Regenerative Medicine Research Program, Department of Dermatology and Cutaneous Surgery and Hussman Institute of Human Genomics, University of Miami Miller Medical School, Miami, FL, USA

    Marjana Tomic-Canic

Authors
  1. Claudia Mimoso
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  2. Ding-Dar Lee
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  3. Jiri Zavadil
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  4. Marjana Tomic-Canic
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  5. Miroslav Blumenberg
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Corresponding author

Correspondence to Miroslav Blumenberg .

Editor information

Editors and Affiliations

  1. Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada

    Kursad Turksen

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Mimoso, C., Lee, DD., Zavadil, J., Tomic-Canic, M., Blumenberg, M. (2013). Analysis and Meta-analysis of Transcriptional Profiling in Human Epidermis. In: Turksen, K. (eds) Epidermal Cells. Methods in Molecular Biology, vol 1195. Springer, New York, NY. https://doi.org/10.1007/7651_2013_60

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  • DOI: https://doi.org/10.1007/7651_2013_60

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  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4939-1223-0

  • Online ISBN: 978-1-4939-1224-7

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