@article{5d32e33d6c2740d3bc4d2b7502a93bc8,
title = "ISLET: individual-specific reference panel recovery improves cell-type-specific inference",
abstract = "We propose a statistical framework ISLET to infer individual-specific and cell-type-specific transcriptome reference panels. ISLET models the repeatedly measured bulk gene expression data, to optimize the usage of shared information within each subject. ISLET is the first available method to achieve individual-specific reference estimation in repeated samples. Using simulation studies, we show outstanding performance of ISLET in the reference estimation and downstream cell-type-specific differentially expressed genes testing. We apply ISLET to longitudinal transcriptomes profiled from blood samples in a large observational study of young children and confirm the cell-type-specific gene signatures for pancreatic islet autoantibody. ISLET is available at https://bioconductor.org/packages/ISLET .",
keywords = "Cell-type-specific differential expression, Deconvolution, Individual-specific reference panel, Temporal measures",
author = "Hao Feng and Guanqun Meng and Tong Lin and Hemang Parikh and Yue Pan and Ziyi Li and Jeffrey Krischer and Qian Li",
note = "Funding Information: This work was partially supported by the National Institutes of Health [U24DK097771 via the NIDDK Information Network{\textquoteright}s (dkNET) New Investigator Pilot Program in Bioinformatics (PI: Q.L.) and Cancer Center Support Grant P30CA21765 to Q.L.; R03CA270725 to Z.L.], the American Cancer Society Institutional Research Grant (ACS IRG) [IRG-16-186-21 to H.F.] through Case Comprehensive Cancer Center, and the Corinne L. Dodero Foundation for the Arts and Sciences and the Case Western Reserve University (CWRU) Program for Autism Education and Research to H.F. and the American Lebanese Syrian Associated Charities (ALSAC) to Q.L. Funding Information: The TEDDY study is funded by the National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Child Health and Human Development, National Institute of Environmental Health Sciences, Centers for Disease Control and Prevention, and JDRF. We thank the TEDDY study data coordinating center at Health Informatics Institute, University of South Florida, for data processing and sharing. The PDBP consortium is supported by the National Institute of Neurological Disorders and Stroke (NINDS) at the National Institutes of Health. A full list of PDBP investigators can be found at https://pdbp.ninds.nih.gov/policy. The PDBP investigators have not participated in reviewing the data analysis or content of the manuscript. Data used in the preparation of this article were obtained from the Accelerating Medicine Partnership (AMP) Parkinson{\textquoteright}s Disease (AMP PD) Knowledge Platform. We thank Lijun Zhang for discussions on PD-related genes and thank Wen Tang for assistance in real data processing. The review history is available as Additional file 6. Anahita Bishop was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. Funding Information: The TEDDY study is funded by the National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Child Health and Human Development, National Institute of Environmental Health Sciences, Centers for Disease Control and Prevention, and JDRF. We thank the TEDDY study data coordinating center at Health Informatics Institute, University of South Florida, for data processing and sharing. The PDBP consortium is supported by the National Institute of Neurological Disorders and Stroke (NINDS) at the National Institutes of Health. A full list of PDBP investigators can be found at https://pdbp.ninds.nih.gov/policy . The PDBP investigators have not participated in reviewing the data analysis or content of the manuscript. Data used in the preparation of this article were obtained from the Accelerating Medicine Partnership (AMP) Parkinson{\textquoteright}s Disease (AMP PD) Knowledge Platform. We thank Lijun Zhang for discussions on PD-related genes and thank Wen Tang for assistance in real data processing. Publisher Copyright: {\textcopyright} 2023, The Author(s).",
year = "2023",
month = dec,
doi = "10.1186/s13059-023-03014-8",
language = "English (US)",
volume = "24",
journal = "Genome biology",
issn = "1474-7596",
publisher = "BioMed Central",
number = "1",
}