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Nucleic Acids Res. 2010 Jul;38(13):4218-30. doi: 10.1093/nar/gkq130. Epub 2010 Mar 22.

Analytical approaches to RNA profiling data for the identification of genes enriched in specific cells.

Author information

1
Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.

Abstract

We have recently developed a novel method for the affinity purification of the complete suite of translating mRNA from genetically labeled cell populations. This method permits comprehensive quantitative comparisons of the genes employed by each specific cell type. We provide a detailed description of tools for analysis of data generated with this and related methodologies. An essential question that arises from these data is how to identify those genes that are enriched in each cell type relative to all others. Genes relatively specifically employed by a cell type may contribute to the unique functions of that cell, and thus may become useful targets for development of pharmacological tools for cell-specific manipulations. We describe here a novel statistic, the specificity index, which can be used for comparative quantitative analysis to identify genes enriched in specific cell populations across a large number of profiles. This measure correctly predicts in situ hybridization patterns for many cell types. We apply this measure to a large survey of CNS cell-specific microarray data to identify those genes that are significantly enriched in each population Data and algorithms are available online (www.bactrap.org).

PMID:
20308160
PMCID:
PMC2910036
DOI:
10.1093/nar/gkq130
[Indexed for MEDLINE]
Free PMC Article

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