Analysis and meta-analysis of transcriptional profiling in human epidermis

Claudia Mimoso, Ding Dar Lee, Jiri Zavadil, Marjana Tomic-Canic, Miroslav Blumenberg

Research output: Chapter in Book/Report/Conference proceedingChapter

7 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationEpidermal Cells
Subtitle of host publicationMethods and Protocols
PublisherHumana Press Inc.
Pages61-97
Number of pages37
ISBN (Print)9781493912230
DOIs
StatePublished - 2014

Publication series

NameMethods in Molecular Biology
Volume1195
ISSN (Print)1064-3745

    Fingerprint

Keywords

  • Affymetrix
  • Annotation
  • Clustering
  • Epidermal differentiation
  • Gene sets
  • Nonparametric
  • Ontological categories
  • Skinomics
  • Transcriptome

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Mimoso, C., Lee, D. D., Zavadil, J., Tomic-Canic, M., & Blumenberg, M. (2014). Analysis and meta-analysis of transcriptional profiling in human epidermis. In Epidermal Cells: Methods and Protocols (pp. 61-97). (Methods in Molecular Biology; Vol. 1195). Humana Press Inc.. https://doi.org/10.1007/7651-2013-60