FastMix: A Versatile Multi-Omics Data Integration Pipeline for Cell Type-Specific Biomarker Inference

Author:

Zhang YunORCID,Sun Hao,Mandava Aishwarya,Aevermann Brian D.,Kollmann Tobias R.,Scheuermann Richard H.,Qiu XingORCID,Qian Yu

Abstract

AbstractWe developed a novel analytic pipeline - FastMix - to integrate flow cytometry, bulk transcriptomics, and clinical covariates for statistical inference of cell type-specific gene expression signatures. FastMix addresses the “large p, small n” problem via a carefully designed linear mixed effects model (LMER), which is applicable for both cross-sectional and longitudinal studies. With a novel moment-based estimator, FastMix runs and converges much faster than competing methods for big data analytics. The pipeline also includes a cutting-edge flow cytometry data analysis method for identifying cell population proportions. Simulation studies showed that FastMix produced smaller type I/II errors with more accurate parameter estimation than competing methods. When applied to real transcriptomics and flow cytometry data in two vaccine studies, FastMix-identified cell type-specific signatures were largely consistent with those obtained from the single cell RNA-seq data, with some unique interesting findings.

Publisher

Cold Spring Harbor Laboratory

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3