@article{e089d135baca404997c201f24585279a,
title = "Pathway-level information extractor (PLIER) for gene expression data",
abstract = "A major challenge in gene expression analysis is to accurately infer relevant biological insights, such as variation in cell-type proportion or pathway activity, from global gene expression studies. We present pathway-level information extractor (PLIER) (https://github.com/wgmao/PLIER and http://gobie.csb.pitt.edu/PLIER), a broadly applicable solution for this problem that outperforms available cell proportion inference algorithms and can automatically identify specific pathways that regulate gene expression. Our method improves interstudy replicability and reveals biological insights when applied to trans-eQTL (expression quantitative trait loci) identification.",
author = "Weiguang Mao and Elena Zaslavsky and Hartmann, {Boris M.} and Sealfon, {Stuart C.} and Maria Chikina",
note = "Funding Information: This work was supported by the US National Institutes of Health (NIH) grants U54HG008540 and 5R03MH109008 to M.C., 1R01HG009299 to M.C. and W.M., and 5U19AI117873 and 5U24DK112331 to Z.E., S.S.C., and H.B.M. The authors acknowledge G. Nudelman for help with RNA-seq processing. This study uses data from dbGaP (phs000486.v1). Funding support for the Genetic Association Information Network (GAIN) Major Depression study: Stage 1 Genome-wide Association In Population Based Samples Study (parent studies: NESDA) and the Netherlands Twin Register (NTR)) was provided by the Netherlands Scientific Organization (904-61-090, 904-61-193, 480-04-004, 400-05-717, Netherlands Organisation for Scientific Research (NWO) Genomics, SPI 56-464-1419), the Centre for Neurogenomics and Cognitive Research (CNCR-VU), the European Union (EU/WLRT-2001-01254), ZonMW (geestkracht program, 10-000-1002), NIMH (RO1 MH059160) and matching funds from participating institutes in NESDA and NTR, and the genotyping of samples was provided through the Genetic Association Information Network (GAIN). The datasets used for the analyses described in this manuscript were obtained from dbGaP (http://www.ncbi. nlm.nih.gov/gap) through dbGaP accession number phs000486.v1.p1. Samples and associated phenotype data for the GAIN Major Depression study: Stage 1 Genome-wide Association In Population Based Samples Study (PI, P. F. Sullivan, University of North Carolina) were provided by D. I. Boomsma and E. de Geus, VU University Amsterdam (PIs NTR), B. W. Penninx, VU University Medical Center Amsterdam, F. Zitman, Leiden University Medical Center, and W. Nolen, University Medical Center Groningen (PIs and site-PIs, NESDA). Publisher Copyright: {\textcopyright} 2019, The Author(s), under exclusive licence to Springer Nature America, Inc.",
year = "2019",
month = jul,
day = "1",
doi = "10.1038/s41592-019-0456-1",
language = "English",
volume = "16",
pages = "607--610",
journal = "Nature Methods",
issn = "1548-7091",
publisher = "Nature Publishing Group",
number = "7",
}