Co-expression module analysis reveals high expression homogeneity for both coding and non-coding genes in sepsis

Liu, Xiaojun; Hong, Chengying; Jiang, Yichun; Li, Wei; Chen, Youlian; Ma, Yonghui; Zhao, Pengfei; Li, Tiyuan; Chen, Huaisheng; Liu, Xueyan; Cheng, Lixin

2023-07-24

10.1186/s12864-023-09460-9

BMC GENOMICS   Impact Factor & Quartile

1471-2164

Sepsis is a life-threatening condition characterized by a harmful host response to infection with organ dysfunction. Annually about 20 million people are dead owing to sepsis and its mortality rates is as high as 20%. However, no studies have been carried out to investigate sepsis from the system biology point of view, as previous research predominantly focused on individual genes without considering their interactions and associations. Here, we conducted a comprehensive exploration of genome-wide expression alterations in both mRNAs and long non-coding RNAs (lncRNAs) in sepsis, using six microarray datasets. Co-expression networks were conducted to identify mRNA and lncRNA modules, respectively. Comparing these sepsis modules with normal modules, we observed a homogeneous expression pattern within the mRNA/lncRNA members, with the majority of them displaying consistent expression direction. Moreover, we identified consistent modules across diverse datasets, consisting of 20 common mRNA members and two lncRNAs, namely CHRM3-AS2 and PRKCQ-AS1, which are potential regulators of sepsis. Our results reveal that the up-regulated common mRNAs are mainly involved in the processes of neutrophil mediated immunity, while the down-regulated mRNAs and lncRNAs are significantly overrepresented in T-cell mediated immunity functions. This study sheds light on the co-expression patterns of mRNAs and lncRNAs in sepsis, providing a novel perspective and insight into the sepsis transcriptome, which may facilitate the exploration of candidate therapeutic targets and molecular biomarkers for sepsis.

Co-expression network Gene module Sepsis Non-coding RNA

SCI

English

First ; Corresponding

Biotechnology & Applied Microbiology ; Genetics & Heredity

Biotechnology & Applied Microbiology ; Genetics & Heredity

WOS:001035790400004

BMC

MOLECULAR BIOLOGY & GENETICS

Web of Science

Southern Univ Sci & Technol, Clin Med Coll 2, Shenzhen Peoples Hosp, Dept Crit Care,Affiliated Hosp 1,Jinan Univ, Shenzhen 518020, Peoples R China

Liu, Xiaojun,Hong, Chengying,Jiang, Yichun,et al. Co-expression module analysis reveals high expression homogeneity for both coding and non-coding genes in sepsis[J]. BMC GENOMICS,2023,24(1).

Liu, Xiaojun.,Hong, Chengying.,Jiang, Yichun.,Li, Wei.,Chen, Youlian.,...&Cheng, Lixin.(2023).Co-expression module analysis reveals high expression homogeneity for both coding and non-coding genes in sepsis.BMC GENOMICS,24(1).

Liu, Xiaojun,et al."Co-expression module analysis reveals high expression homogeneity for both coding and non-coding genes in sepsis".BMC GENOMICS 24.1(2023).