Measuring single-cell level gene expression stability and variability in healthy and severe COVID-19 patients using Kullback-Leibler divergence

Inseung Hwang; Jaeyeon Jang; Kwangsoo Kim; Hye Yeong Jo; Sang Cheol Kim; Inuk Jung

doi:10.1109/BIBM55620.2022.9995123

Measuring single-cell level gene expression stability and variability in healthy and severe COVID-19 patients using Kullback-Leibler divergence

Inseung Hwang, Jaeyeon Jang, Kwangsoo Kim, Hye Yeong Jo, Sang Cheol Kim, Inuk Jung

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Recent advances in single-cell RNA sequencing (scRNA-seq) technology have enabled the acquisition of RNA at the single-cell level, which showed that the expression level of genes is highly variable across and within the cell types. Even well-known housekeeping genes showed high expression variance in a single condition and within the same cell types. Previous studies made efforts to identify stably expressed genes and use them as a yardstick for robust gene expression normalization. On the other hand, drugs were shown to be less effective on genes with high expression variance. Thus, identifying both stably and variably expressed genes is an important task, especially at the single-cell level. In this study, using the Kullback-Leibler divergence method, we proposed a metric to measure the expression stability of each gene. Using private scRNA-seq data composed of 25 severe COVID-19 patients and 40 healthy individuals, we identified variably expressed genes specific to COVID-19-infected patients and healthy cohorts.

Original language	English
Title of host publication	Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022
Editors	Donald Adjeroh, Qi Long, Xinghua Shi, Fei Guo, Xiaohua Hu, Srinivas Aluru, Giri Narasimhan, Jianxin Wang, Mingon Kang, Ananda M. Mondal, Jin Liu
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	3818-3820
Number of pages	3
ISBN (Electronic)	9781665468190
DOIs	https://doi.org/10.1109/BIBM55620.2022.9995123
State	Published - 2022
Event	2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022 - Las Vegas, United States Duration: 6 Dec 2022 → 8 Dec 2022

Publication series

Name	Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022

Conference

Conference	2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022
Country/Territory	United States
City	Las Vegas
Period	6/12/22 → 8/12/22

Keywords

COVID-19
Gene expression stability
Single-cell

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1109/BIBM55620.2022.9995123

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Hwang, I., Jang, J., Kim, K., Jo, H. Y., Kim, S. C., & Jung, I. (2022). Measuring single-cell level gene expression stability and variability in healthy and severe COVID-19 patients using Kullback-Leibler divergence. In D. Adjeroh, Q. Long, X. Shi, F. Guo, X. Hu, S. Aluru, G. Narasimhan, J. Wang, M. Kang, A. M. Mondal, & J. Liu (Eds.), Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022 (pp. 3818-3820). (Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM55620.2022.9995123

Hwang, Inseung ; Jang, Jaeyeon ; Kim, Kwangsoo et al. / Measuring single-cell level gene expression stability and variability in healthy and severe COVID-19 patients using Kullback-Leibler divergence. Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022. editor / Donald Adjeroh ; Qi Long ; Xinghua Shi ; Fei Guo ; Xiaohua Hu ; Srinivas Aluru ; Giri Narasimhan ; Jianxin Wang ; Mingon Kang ; Ananda M. Mondal ; Jin Liu. Institute of Electrical and Electronics Engineers Inc., 2022. pp. 3818-3820 (Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022).

@inproceedings{bb2da57c83b54535af09a11eb853cd2a,

title = "Measuring single-cell level gene expression stability and variability in healthy and severe COVID-19 patients using Kullback-Leibler divergence",

abstract = "Recent advances in single-cell RNA sequencing (scRNA-seq) technology have enabled the acquisition of RNA at the single-cell level, which showed that the expression level of genes is highly variable across and within the cell types. Even well-known housekeeping genes showed high expression variance in a single condition and within the same cell types. Previous studies made efforts to identify stably expressed genes and use them as a yardstick for robust gene expression normalization. On the other hand, drugs were shown to be less effective on genes with high expression variance. Thus, identifying both stably and variably expressed genes is an important task, especially at the single-cell level. In this study, using the Kullback-Leibler divergence method, we proposed a metric to measure the expression stability of each gene. Using private scRNA-seq data composed of 25 severe COVID-19 patients and 40 healthy individuals, we identified variably expressed genes specific to COVID-19-infected patients and healthy cohorts.",

keywords = "COVID-19, Gene expression stability, Single-cell",

author = "Inseung Hwang and Jaeyeon Jang and Kwangsoo Kim and Jo, {Hye Yeong} and Kim, {Sang Cheol} and Inuk Jung",

note = "Publisher Copyright: {\textcopyright} 2022 IEEE.; 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022 ; Conference date: 06-12-2022 Through 08-12-2022",

year = "2022",

doi = "10.1109/BIBM55620.2022.9995123",

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series = "Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "3818--3820",

editor = "Donald Adjeroh and Qi Long and Xinghua Shi and Fei Guo and Xiaohua Hu and Srinivas Aluru and Giri Narasimhan and Jianxin Wang and Mingon Kang and Mondal, {Ananda M.} and Jin Liu",

booktitle = "Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022",

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Hwang, I, Jang, J, Kim, K, Jo, HY, Kim, SC & Jung, I 2022, Measuring single-cell level gene expression stability and variability in healthy and severe COVID-19 patients using Kullback-Leibler divergence. in D Adjeroh, Q Long, X Shi, F Guo, X Hu, S Aluru, G Narasimhan, J Wang, M Kang, AM Mondal & J Liu (eds), Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022. Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022, Institute of Electrical and Electronics Engineers Inc., pp. 3818-3820, 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022, Las Vegas, United States, 6/12/22. https://doi.org/10.1109/BIBM55620.2022.9995123

Measuring single-cell level gene expression stability and variability in healthy and severe COVID-19 patients using Kullback-Leibler divergence. / Hwang, Inseung; Jang, Jaeyeon; Kim, Kwangsoo et al.
Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022. ed. / Donald Adjeroh; Qi Long; Xinghua Shi; Fei Guo; Xiaohua Hu; Srinivas Aluru; Giri Narasimhan; Jianxin Wang; Mingon Kang; Ananda M. Mondal; Jin Liu. Institute of Electrical and Electronics Engineers Inc., 2022. p. 3818-3820 (Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Measuring single-cell level gene expression stability and variability in healthy and severe COVID-19 patients using Kullback-Leibler divergence

AU - Hwang, Inseung

AU - Jang, Jaeyeon

AU - Kim, Kwangsoo

AU - Jo, Hye Yeong

AU - Kim, Sang Cheol

AU - Jung, Inuk

PY - 2022

Y1 - 2022

N2 - Recent advances in single-cell RNA sequencing (scRNA-seq) technology have enabled the acquisition of RNA at the single-cell level, which showed that the expression level of genes is highly variable across and within the cell types. Even well-known housekeeping genes showed high expression variance in a single condition and within the same cell types. Previous studies made efforts to identify stably expressed genes and use them as a yardstick for robust gene expression normalization. On the other hand, drugs were shown to be less effective on genes with high expression variance. Thus, identifying both stably and variably expressed genes is an important task, especially at the single-cell level. In this study, using the Kullback-Leibler divergence method, we proposed a metric to measure the expression stability of each gene. Using private scRNA-seq data composed of 25 severe COVID-19 patients and 40 healthy individuals, we identified variably expressed genes specific to COVID-19-infected patients and healthy cohorts.

AB - Recent advances in single-cell RNA sequencing (scRNA-seq) technology have enabled the acquisition of RNA at the single-cell level, which showed that the expression level of genes is highly variable across and within the cell types. Even well-known housekeeping genes showed high expression variance in a single condition and within the same cell types. Previous studies made efforts to identify stably expressed genes and use them as a yardstick for robust gene expression normalization. On the other hand, drugs were shown to be less effective on genes with high expression variance. Thus, identifying both stably and variably expressed genes is an important task, especially at the single-cell level. In this study, using the Kullback-Leibler divergence method, we proposed a metric to measure the expression stability of each gene. Using private scRNA-seq data composed of 25 severe COVID-19 patients and 40 healthy individuals, we identified variably expressed genes specific to COVID-19-infected patients and healthy cohorts.

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KW - Gene expression stability

KW - Single-cell

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DO - 10.1109/BIBM55620.2022.9995123

M3 - Conference contribution

AN - SCOPUS:85146733662

T3 - Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022

SP - 3818

EP - 3820

BT - Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022

A2 - Adjeroh, Donald

A2 - Long, Qi

A2 - Shi, Xinghua

A2 - Guo, Fei

A2 - Hu, Xiaohua

A2 - Aluru, Srinivas

A2 - Narasimhan, Giri

A2 - Wang, Jianxin

A2 - Kang, Mingon

A2 - Mondal, Ananda M.

A2 - Liu, Jin

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022

Y2 - 6 December 2022 through 8 December 2022

ER -

Hwang I, Jang J, Kim K, Jo HY, Kim SC, Jung I. Measuring single-cell level gene expression stability and variability in healthy and severe COVID-19 patients using Kullback-Leibler divergence. In Adjeroh D, Long Q, Shi X, Guo F, Hu X, Aluru S, Narasimhan G, Wang J, Kang M, Mondal AM, Liu J, editors, Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022. Institute of Electrical and Electronics Engineers Inc. 2022. p. 3818-3820. (Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022). doi: 10.1109/BIBM55620.2022.9995123

Measuring single-cell level gene expression stability and variability in healthy and severe COVID-19 patients using Kullback-Leibler divergence

Abstract

Publication series

Conference

Keywords

UN SDGs

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