An association study of clock genes with major depressive disorder

小桶 基因 生物 时钟 计算生物学 重性抑郁障碍 基因调控网络 遗传学 基因表达 转录组 神经科学 认知
作者
Ying Li,Peidong Miao,Fang Li,Jinsong Huang,Lijun Fan,Qiaoling Chen,Yunan Zhang,Yan Feng,Yan Gao
出处
期刊:Journal of Affective Disorders [Elsevier BV]
卷期号:341: 147-153 被引量:6
标识
DOI:10.1016/j.jad.2023.08.113
摘要

To study the relationship between clock genes and Major Depressive Disorder (MDD).GEO database was used to obtain the chip data and clinical information of datasets GSE98793, GSE39653 and GSE52790. The differentially expressed clock genes were found through the analysis of the differentially expressed genes between MDD and healthy controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) enrichment analysis were performed on the differential expressed clock genes. Lasso Regression and Support Vector Machine (SVM) method were used for screening the differential expressed clock genes. Logistic regression was used to establish a diagnostic model for depression with the screened genes. Receiver Operating Characteristic (ROC) Curve was used to verify the model. Gene differential expression analysis was performed for MDD with high scores and MDD with low scores in the diagnostic model. Gene Set Enrichment Analysis (GSEA) enrichment analysis was performed for differentially expressed genes. Single-gene GSEA was used to analyze each gene in the model separately. Cibersort method was used to analyze the immune infiltration of MDD and healthy controls, and the correlation between immune cells and clock genes was analyzed. Cytoscape was used to analyze the clock gene interaction network. The DGIdb website was used to predict potentially effective therapeutic drugs for clock genes closely related to MDD.Six genes were identified by differential expression analysis of clock genes between MDD and healthy controls. GO and KEGG enrichment analysis of 6 genes showed that their pathways were concentrated such as circadian rhythm, rhythmic process, TGF - beta signaling pathway, longevity regulating pathway-multiple species, adipocytokine signaling pathway and so on. Lasso regression and SVM were used to screen out 5 clock genes (HDAC1, ID3, NFIL3, PRKAA1, TNF) for MDD. The diagnostic model of depression was established according to the 5 clock genes. The area under the curve (AUC) of the established depression diagnostic model was 0.686. Gene difference analysis was performed between MDD patients with high score of clock gene diagnostic model and MDD patients with low score. GSEA was performed for the differential genes showed that the most enriched pathways were:adipocytokine signaling pathway, TGF beta signaling pathway, oxidative phosphorylation, primary immunodeficiency, and so on. The single gene GSEA showed that the most enriched pathways were Toll like receptor signaling pathway, glucolipid metabolism, amino acid metabolism, neuroactive ligand receptor interaction, and so on. The results of immune infiltration analysis showed that NK cells resting and Macrophages M2 were different between MDD and control groups. In MDD, the gene closely related to NK cells resting was HDAC1, and the genes closely related to Macrophages M2 were HDAC1 and NFIL3. The RNA interactions network of clock genes shows that the regulation process is complex, which can provide a reference for subsequent related research. Potential therapeutic drugs predict display, among the 5 clock genes, TNF, HDAC1, and PRKAA1 may have potential effective therapeutic drugs.Among all CLOCK genes, HDAC1, ID3, NFIL3, PRKAA1, TNF are closely related to MDD. Among them, TNF, HDAC1, and PRKAA1 may have potential effective therapeutic drugs.
最长约 10秒,即可获得该文献文件

科研通智能强力驱动
Strongly Powered by AbleSci AI
更新
PDF的下载单位、IP信息已删除 (2025-6-4)

科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
意未清完成签到,获得积分10
刚刚
陈淑玲发布了新的文献求助10
1秒前
天天快乐应助跳跃的寄瑶采纳,获得10
2秒前
风中垣完成签到,获得积分10
2秒前
2秒前
3秒前
咔咔完成签到,获得积分10
5秒前
科研通AI5应助九品炼丹师采纳,获得10
5秒前
6秒前
白桥发布了新的文献求助10
6秒前
7秒前
深情安青应助如7而至采纳,获得10
7秒前
7秒前
8秒前
pb完成签到,获得积分10
8秒前
blue完成签到,获得积分10
9秒前
无恙发布了新的文献求助10
9秒前
科研通AI5应助hey采纳,获得10
9秒前
10秒前
领导范儿应助浅渊采纳,获得10
10秒前
复杂之桃完成签到,获得积分10
11秒前
Nikko发布了新的文献求助10
12秒前
12秒前
管靖易完成签到 ,获得积分10
12秒前
13秒前
跳跃的寄瑶完成签到,获得积分10
13秒前
14秒前
Akim应助Giinjju采纳,获得10
14秒前
14秒前
yydragen应助Adzuki0812采纳,获得20
15秒前
15秒前
15秒前
16秒前
DAYDAY完成签到 ,获得积分10
16秒前
lwei完成签到 ,获得积分20
16秒前
17秒前
白桥完成签到,获得积分10
17秒前
17秒前
17秒前
lele发布了新的文献求助10
18秒前
高分求助中
A new approach to the extrapolation of accelerated life test data 1000
Picture Books with Same-sex Parented Families: Unintentional Censorship 700
ACSM’s Guidelines for Exercise Testing and Prescription, 12th edition 500
Nucleophilic substitution in azasydnone-modified dinitroanisoles 500
不知道标题是什么 500
Indomethacinのヒトにおける経皮吸収 400
Effective Learning and Mental Wellbeing 400
热门求助领域 (近24小时)
化学 材料科学 医学 生物 工程类 有机化学 生物化学 物理 内科学 纳米技术 计算机科学 化学工程 复合材料 遗传学 基因 物理化学 催化作用 冶金 细胞生物学 免疫学
热门帖子
关注 科研通微信公众号,转发送积分 3975922
求助须知:如何正确求助?哪些是违规求助? 3520226
关于积分的说明 11201711
捐赠科研通 3256720
什么是DOI,文献DOI怎么找? 1798423
邀请新用户注册赠送积分活动 877576
科研通“疑难数据库(出版商)”最低求助积分说明 806452