Screening of differentially expressed genes in children with cerebral palsy and the construction of a network of the effective components of traditional Chinese medicine

Abstract

Background: The study sought to construct a network of the effective components of traditional Chinese medicine (TCM) and potential therapeutic target genes of cerebral palsy based on data sets from highthroughput sequencing and the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP).Methods: A transcriptome sequencing data set (GSE183021) of blood samples from children with cerebral palsy was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between the cerebral palsy blood samples and control blood samples were screened. The TCM active components and target genes were identified from the TCMSP. We constructed a network of the active ingredients of TCM and the cerebral palsy DEGs.Results: Using a |log2 fold change| ≥1 and a false discovery rate <0.05 as the screening criteria for the blood samples of 5 children with cerebral palsy and 5 control participants, 399 DEGs were identified. In the cerebral palsy blood samples, 209 genes were upregulated, and 190 genes were downregulated. The effective components of Angelica sinensis, Shenjincao, and Achyranthes bidentata, targeted 158 genes, and 49 genes crossed with the cerebral palsy DEGs. A network was constructed with the active ingredients of Angelica sinensis, Shenjincao, and Achyranthes bidentata and the DEGs of the cerebral palsy as nodes. Interleukin (IL)-1β, IL-6, prostaglandin-endoperoxide synthase 1, tumor necrosis factor, estrogen receptor 1, and nitric oxide synthase 2 had a wide range of effects on the effective components of Angelica sinensis, Shenjincao, and Achyranthes bidentata. Conclusions:The effective components of Angelica sinensis, Shenjincao, Achyranthes sinensis, and interact closely with the cerebral palsy DEGs. Based on the interaction network, the pharmacological mechanism of TCM in the treatment of cerebral palsy can be elucidated and new therapeutic targets discovered.

Diagnosis and therapies for patients with cerebral palsy over the past 30 years: a bibliometric analysis

“…We downloaded canonical pathway gene sets based on the Reactome pathway database from the GSEA database ( 7 ). The pathway enrichment analysis of the GSE183021 ( 8 ) dataset was performed using the GSVA R package ( 9 ). The differential gene expression analysis of pathway scores was performed based on the limma R package ( 10 ).…”

Bioinformatics-based discovery of biomarkers and immunoinflammatory targets in children with cerebral palsy: An observational study

“…The chip data of GSE183021 were studied on 5 children with CP and 5 healthy twins to eliminate interfering factors (average age: 3.3 ± 1.5, average birth weight: 2.9 ± 0.4 kg). [14] GPL29703 is a sequencing data platform for data, all of which use the human body as the source. [14] Use the "limma" tool of Sangerbox 3.0 to perform differential gene analysis to clarify the differential genes between CP samples and control samples to study the impact of differences in related gene expression levels in CP patients.…”

“…[14] GPL29703 is a sequencing data platform for data, all of which use the human body as the source. [14] Use the "limma" tool of Sangerbox 3.0 to perform differential gene analysis to clarify the differential genes between CP samples and control samples to study the impact of differences in related gene expression levels in CP patients. [15] The threshold for differential genes was set to a 1.5-fold difference and P value < .05.…”

“…[12,13] With the increasing number of related studies on CP gene expression profiles and the establishment of various public databases year by year, bioinformatics methods can be used to conduct deeper research on CP, thereby expanding the understanding of the pathological mechanisms of CP. [14] This study collected genetic data from children with CP to obtain differentially expressed genes of CP. Based on this, bioinformatics analysis was performed and the core driver genes of CP were screened out to provide direction for further research.…”