Work

CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types

Year: 2016

Type: article

Abstract: We present a sensitive approach to predict genes expressed selectively in specific cell types, by searching publicly available expression data for genes with a similar expression profile to known cell-specific markers. Our method, CellMapper, strongly outperforms previous computational algorithms to predict cell type-specific expression, especially for rare and difficult-to-isolate cell types. Furthermore, CellMapper makes accurate predictions for human brain cell types that have never been isolated, and can be rapidly applied to diverse cell types from many tissues. We demonstrate a clinically relevant application to prioritize candidate genes in disease susceptibility loci identified by GWAS.

Source: Genome biology

DOI: 10.1186/s13059-016-1062-5

Authors: Bradlee D. Nelms, Levi Waldron, Luis A. Barrera, Andrew W. Weflen, Jeremy A. Goettel, Guoji Guo, Robert K. Montgomery, Marian R. Neutra, David T. Breault, Scott B. Snapper, Stuart H. Orkin, Martha L. Bulyk, Curtis Huttenhower, Wayne I. Lencer

Institutions: Boston Children's Hospital, Harvard University, City University of New York, Brigham and Women's Hospital, Zhejiang University, Dana-Farber Cancer Institute, Harvard Stem Cell Institute

Language: English

Topic: Gene expression and cancer classification

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $5,490

Funders: National Science Foundation, National Institutes of Health, Harvard Digestive Diseases Center, Harvard University, National Human Genome Research Institute, National Cancer Institute, National Institute of Diabetes and Digestive and Kidney Diseases

Awards: Mechanism of action for the epithelial-specific ER stress sensor IRE1β in regulating intestinal homeostasis and host defense, G1444796925, Characterization of Telomerase Expressing Intestinal Stem Cells, FcRn-dependent sorting of IgG and IgG-opsinized antigens by epithelial cells, High-Resolution Analysis of Transcription Factors' DNA Binding Specificities, Intestinal Disease-enterocyte toxin interaction, G5308886365, G5857948765, G6325015508, G9000037087, G9000145084, Integrated Epithelial and Muscosal Biology, Dana-Farber/Harvard Cancer Center

OpenAlex ID: W2527229715

FWCI: 1.558

Cites: 55

Cited by: 24

Related to: 10