Dataset Information

Constructing a 10-core genes panel for diagnosis of pediatric sepsis.

ABSTRACT:

Background

The lack of sensitivity and specificity of most biomarkers or the lack of relevant studies to demonstrate their effectiveness in sepsis.

Methods

Downloaded three sets of sepsis expression data (GSE13904, GSE25504, GSE26440) from GEO. Then, using the R limma package and WGCNA analysis tocore genes. Finally, the value of these core genes was confirmed by clinical samples.

Results

Compared to normal samples, we obtain many abnormally expressed genes in the pediatric sepsis. WGCNA co-expression analysis showed that genes from blue and turquoise module were close correlation with pediatric sepsis. The top 20 genes (TIMP2, FLOT1, HCK, NCF4, SERPINA1, IL17RA, PGD, PRKCD, GLT1D1, ALOX5, SIRPA, DOK3, ITGAM, S100A11, ZNF438, PLIN3, LTB4R, TSPO, MAPK14, GAS7) of the blue module of pediatric sepsis were mainly enriched in neutrophil degranulation, etc The top 20 genes (TBC1D4, NOL11, NLRC3, ZNF121, DYRK2, ABCE1, MAGEH1, TMEM263, MCUB, MALT1, DDHD2, TRAC, NOC3L, LCK, TRMT61B, ZNF260, ENOPH1, LOC93622, NAE1, TRBC1) for turquoise module were mainly enriched in rRNA-containing ribonucleoprotein complexes exported from the nucleus, etc The selected hub gene of pediatric sepsis was combined with the markers of cell surface and found 10 core genes (HCK, PRKCD, SIRPA, DOK3, ITGAM, LTB4R, MAPK14, MALT1, NLRC3, LCK). ROC showed that AUC of the 10 core genes for diagnosis of pediatric sepsis was above 0.9.

Conclusion

There were many abnormally expressed genes in patients with pediatric sepsis. The panel constructed by the 10 core genes was expected to become a biomarker panel for clinical application of pediatric sepsis.

SUBMITTER: Zhou X

PROVIDER: S-EPMC7958006 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Publications

Constructing a 10-core genes panel for diagnosis of pediatric sepsis.

Zhou Xiaojie X Wang Yumin Y Chen Jie J Pan Jingye J

Journal of clinical laboratory analysis 20201203 3

<h4>Background</h4>The lack of sensitivity and specificity of most biomarkers or the lack of relevant studies to demonstrate their effectiveness in sepsis.<h4>Methods</h4>Downloaded three sets of sepsis expression data (GSE13904, GSE25504, GSE26440) from GEO. Then, using the R limma package and WGCNA analysis tocore genes. Finally, the value of these core genes was confirmed by clinical samples.<h4>Results</h4>Compared to normal samples, we obtain many abnormally expressed genes in the pediatric ...[more]

PMID: 33274532

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Project description:Sepsis, a life-threatening disease caused by dysregulated host response to infection, is a major public health problem with a high mortality and morbidity rate. Pyroptosis is a new type of programmed cell death discovered in recent years, which has been proved to play an important role in sepsis. Nevertheless, there is no comprehensive report, which can help researchers get a quick overview and find research hotspots. Thus, we aimed to identify the study status and knowledge structures of pyroptosis in sepsis and summarize the key mechanism of pyroptosis in sepsis. The data were retrieved and downloaded from the WOS database. Software such as VOSviewer was used to analyze these publications. Key genes were picked out by using (https://www.genecards.org) and (http://www.bioinformatics.com). Then, Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to performed these key genes. From 2011 to 2021, a total of 299 papers met the search criteria, and the global interest in pyroptosis in sepsis measured by the value of (RRI) has started to increase since 2016. China ranked first in the number of publications, followed by the USA. The journal Frontiers in Immunology published the most relevant articles. Through keyword co-occurrence analysis, the high-frequency subject terms were divided into three clusters like "animal research", "cell research," and "molecular research" clusters. "mir," "aki," "monocyte," and "neutrophil" were the newest keywords that may be the hotspot. In addition, a total of 15 genes were identified as hub genes. TNF, IL-1β, AKT1, CASP1, and STAT3 were highly expressed in lung tissues, thymus tissues, and lymphocytes. KEGG analysis indicated that pyroptosis may play a vital role in sepsis via the NOD, PI3K/AKT, and MAPK/JNK pathways. Through the quantitative analysis of the literature on pyroptosis in sepsis, we revealed the current status and hotspots of research in this field and provided some guidance for further studies.

Dataset Information

Constructing a 10-core genes panel for diagnosis of pediatric sepsis.

Background

Methods

Results

Conclusion

Publications

Constructing a 10-core genes panel for diagnosis of pediatric sepsis.

Similar Datasets

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