Analysis and meta-analysis of transcriptional profiling in human epidermis

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

Research output: Contribution to journalArticle

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)
Pages (from-to)61-97
Number of pages37
JournalMethods in molecular biology (Clifton, N.J.)
Volume1195
DOIs
StatePublished - 2014
Externally publishedYes

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Epidermis
Meta-Analysis
Skin
Genes
Molecular Sequence Annotation
Inborn Genetic Diseases
Oligonucleotide Array Sequence Analysis
Computational Biology
Keratinocytes
Psoriasis
Genetic Promoter Regions
Cell Differentiation
Melanoma
Transcription Factors
Stem Cells
Binding Sites
Research Personnel
Inflammation
Carcinoma
Wounds and Injuries

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Analysis and meta-analysis of transcriptional profiling in human epidermis. / Mimoso, Claudia; Lee, Ding Dar; Zavadil, Jiri; Tomic-Canic, Marjana; Blumenberg, Miroslav.

In: Methods in molecular biology (Clifton, N.J.), Vol. 1195, 2014, p. 61-97.

Research output: Contribution to journalArticle

Mimoso, Claudia ; Lee, Ding Dar ; Zavadil, Jiri ; Tomic-Canic, Marjana ; Blumenberg, Miroslav. / Analysis and meta-analysis of transcriptional profiling in human epidermis. In: Methods in molecular biology (Clifton, N.J.). 2014 ; Vol. 1195. pp. 61-97.
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