CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-12

AUTHORS

Jason E Shoemaker, Tiago JS Lopes, Samik Ghosh, Yukiko Matsuoka, Yoshihiro Kawaoka, Hiroaki Kitano

ABSTRACT

BACKGROUND: Interpreting in vivo sampled microarray data is often complicated by changes in the cell population demographics. To put gene expression into its proper biological context, it is necessary to distinguish differential gene transcription from artificial gene expression induced by changes in the cellular demographics. RESULTS: CTen (cell type enrichment) is a web-based analytical tool which uses our highly expressed, cell specific (HECS) gene database to identify enriched cell types in heterogeneous microarray data. The web interface is designed for differential expression and gene clustering studies, and the enrichment results are presented as heatmaps or downloadable text files. CONCLUSIONS: In this work, we use an independent, cell-specific gene expression data set to assess CTen's performance in accurately identifying the appropriate cell type and provide insight into the suggested level of enrichment to optimally minimize the number of false discoveries. We show that CTen, when applied to microarray data developed from infected lung tissue, can correctly identify the cell signatures of key lymphocytes in a highly heterogeneous environment and compare its performance to another popular bioinformatics tool. Furthermore, we discuss the strong implications cell type enrichment has in the design of effective microarray workflow strategies and show that, by combining CTen with gene expression clustering, we may be able to determine the relative changes in the number of key cell types.CTen is available at http://www.influenza-x.org/~jshoemaker/cten/ More... »

PAGES

460

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Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-13-460

DOI

http://dx.doi.org/10.1186/1471-2164-13-460

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PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22953731


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