Document Type
Article
Publication Date
6-22-2020
Keywords
JGM, JAXCC
JAX Source
Genome Biol 2020 Jun 22; 21(1):150
Volume
21
Issue
1
First Page
150
Last Page
150
ISSN
1474-760X
PMID
32571363
DOI
https://doi.org/10.1186/s13059-020-02033-z
Abstract
Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma. RNA sequencing (RNA-seq) of sputum samples can be challenging to interpret due to the complex and heterogeneous mixtures of human cells and exogenous (microbial) material. In this study, we develop a pipeline that integrates dimensionality reduction and statistical modeling to grapple with the heterogeneity. LDA(Latent Dirichlet allocation)-link connects microbes to genes using reduced-dimensionality LDA topics. We validate our method with single-cell RNA-seq and microscopy and then apply it to the sputum of asthmatic patients to find known and novel relationships between microbes and genes.
Recommended Citation
Spakowicz D,
Lou S,
Barron B,
Gomez J,
Li T,
Liu Q,
Grant N,
Yan X,
Hoyd R,
Weinstock GM,
Chupp G,
Gerstein M.
Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients. Genome Biol 2020 Jun 22; 21(1):150
Comments
This article is licensed under a Creative Commons Attribution 4.0 International License.