Multiple Transcriptome Data Analysis Reveals Biologically Relevant Atopic Dermatitis Signature Genes and Pathways

Debajyoti Ghosh, Lili Ding, Umasundari Sivaprasad, Esmond Geh, Jocelyn Biagini Myers, Jonathan A Bernstein, Gurjit K Khurana Hershey and Tesfaye B Mersha

PLOS ONE, 2015, vol. 10, issue 12, 1-23

Abstract: Several studies have identified genes that are differentially expressed in atopic dermatitis (AD) compared to normal skin. However, there is also considerable variation in the list of differentially expressed genes (DEGs) reported by different groups and the exact cause of AD is still not fully understood. Using a rank-based approach, we analyzed gene expression data from five different microarray studies, comprising a total of 127 samples and more than 250,000 transcripts. A total of 89 AD gene expression signatures ‘89ADGES’, including FLG gene, were identified to show dysregulation consistently across these studies. Using a Support Vector Machine, we showed that the ‘89ADGES’ discriminates AD from normal skin with 98% predictive accuracy. Functional annotation of these genes implicated their roles in immune responses (e.g., betadefensin, microseminoprotein), keratinocyte differentiation/epidermal development (e.g., FLG, CORIN, AQP, LOR, KRT16), inflammation (e.g., IL37, IL27RA, CCL18) and lipid metabolism (e.g., AKR1B10, FAD7, FAR2). Subsequently, we validated a subset of signature genes using quantitative PCR in a mouse model. Using a bioinformatic approach, we identified keratinocyte pathway over-represented (P =

Date: 2015
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0144316

DOI: 10.1371/journal.pone.0144316

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