| Literature DB >> 33021140 |
Jun Shen1,2, Xiao-Chang Chen3, Wang-Jun Li4, Qiu Han5, Chun Chen3, Jing-Min Lu2, Jin-Yu Zheng2, Shou-Ru Xue1.
Abstract
OBJECTIVE: To identify Parkinson's disease (PD)-associated deregulated pathways and genes, to further elucidate the pathogenesis of PD.Entities:
Keywords: Parkinson’s disease; clustering analysis; deregulated pathway; differentially expressed gene; genetic risk factors; protein–protein interactions; support vector machine model
Mesh:
Year: 2020 PMID: 33021140 PMCID: PMC7543192 DOI: 10.1177/0300060520957197
Source DB: PubMed Journal: J Int Med Res ISSN: 0300-0605 Impact factor: 1.671
Figure 1.Statistical analysis and clustering of differentially expressed genes (DEGs) in Parkinson’s disease (PD). (a) Volcano plot of the DEGs. (b) Sample hierarchical clustering based on the expression of the DEGs. (c) Consensus cumulative distribution function (CDF) under different clustering numbers of DEGs. A larger CDF indicates a better gene clustering effect. When k = 2, the clustering result was the best. (d) The area difference value (delta area) between two CDF curves and the horizontal axis. k = 3 was the largest k with an appreciable increase in consensus. (e) Distribution of the clustering results shown by an item tracking plot. When k = 2, the number of mixed elements was the smallest.
Figure 2.Gene enrichment results of cluster 1 genes (a) and cluster 2 genes (b). The horizontal axis shows the number of genes. The gray solid line represents –lg(P-value).
Significantly deregulated pathways between Parkinson’s disease and control samples.
| Pathway | |
|---|---|
| hsa04060:Cytokine–cytokine receptor interaction | 0.025838 |
| hsa04062:Chemokine signaling pathway | 0.02773 |
| hsa04145:Phagosome | 0.032876 |
| hsa04810:Regulation of actin cytoskeleton | 0.03367 |
| hsa04144:Endocytosis | 0.03721 |
| hsa04540:Gap junction | 0.038855 |
| hsa04510:Focal adhesion | 0.042322 |
| hsa04611:Platelet activation | 0.049717 |
| hsa04640:Hematopoietic cell lineage | 0.053322 |
| hsa04022:cGMP–PKG signaling pathway | 0.054027 |
| hsa04512:ECM–receptor interaction | 0.058062 |
| hsa00230:Purine metabolism | 0.059821 |
The 39 differentially expressed genes in the eight significantly deregulated pathways between Parkinson’s disease patients and controls.
| Gene | logFC | Gene | logFC | Gene | logFC |
|---|---|---|---|---|---|
|
| 0.746 |
| 0.688 |
| 0.856 |
|
| 0.706 |
| −0.195 |
| 0.690 |
|
| 0.588 |
| 0.631 |
| 0.589 |
|
| 0.622 |
| 1.284 |
| 1.162 |
|
| 0.600 |
| 0.922 |
| 0.885 |
|
| 0.754 |
| 0.827 |
| 1.417 |
|
| 1.720 |
| 0.808 |
| 1.232 |
|
| 0.752 |
| 1.253 |
| 1.185 |
|
| 1.234 |
| 0.680 |
| 1.529 |
|
| 1.020 |
| 1.454 |
| 1.108 |
|
| 1.096 |
| 1.059 |
| 0.980 |
|
| 1.435 |
| 0.766 |
| 1.531 |
|
| 1.430 |
| 1.008 |
| 1.554 |
FC, fold change.
Figure 3.The protein–protein interaction (PPI) network and analysis of the 10 hub genes. (a) PPI network of the genes enriched in the significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Pink nodes represent the 10 hub genes. A larger node size indicates a higher degree of interaction. (b) Receiver operating characteristic (ROC) curve analysis of the SVM model for predicting disease status in the GSE100054 dataset. (c) The log2(fold change) value of the 10 hub genes in the validation dataset (GSE49126) and study dataset (GSE100054). (d) Relative expression levels of the 10 genes in Parkinson’s disease (PD) and controls in the patient cohort.
The demographic characteristics of the Parkinson’s disease patients and controls.
| Variables | Parkinson’s disease | Control | |
|---|---|---|---|
| GSE100054 | ( | ( | |
| Age (years) | 67.00 ± 8.89 | 62.33 ± 7.50 | 0.211b |
| Sex ratio (male/female) | 5/4 | 5/5 | 1.000a |
| Validation cohort | |||
| Age (years) | 67.10 ± 11.20 | 65.51 ± 8.77 | 0.463b |
| Sex ratio (male/female) | 54/49 | 16/15 | 1.000a |
| Duration (years) | 6.93 ± 2.23 | 0 | |
| Hoehn and Yahr stage | 2.61 ± 0.64 (range 1–4) | 0 |
aχ2 test; bMann–Whitney U test.
Association between genes and Parkinson’s disease status in the GSE100054 dataset and validation cohort.
| Variable | GSE100054 ( | Validation cohort
( | ||||||
|---|---|---|---|---|---|---|---|---|
| β | OR | 95% CI | β | OR | 95% CI | |||
|
| 2.191 | 12.075 | 1.159–125.786 | 0.037 | 0.175 | 2.574 | 0.286–2.470 | 0.752 |
|
| 1.325 | 3.761 | 1.106–12.793 | 0.034 | 2.568 | 6.526 | 2.885–13.455 |
|
|
| 2.608 | 13.576 | 1.040–177.137 | 0.047 | 2.365 | 8.636 | 1.630–15.676 |
|
|
| 1.740 | 5.699 | 0.966–33.618 | 0.055 | 0.366 | 1.998 | 0.354–2.809 | 0.996 |
|
| 0.815 | 2.260 | 0.982–5.199 | 0.055 | 0.533 | 1.704 | 0.581–5.002 | 0.332 |
|
| 0.719 | 2.051 | 0.968–4.346 | 0.061 | 0.063 | 1.725 | 0.873–40.162 | 0.435 |
|
| 1.926 | 6.862 | 1.173–40.162 | 0.033 | 1.260 | 3.526 | 1.249–9.957 |
|
|
| 1.341 | 3.822 | 1.260–11.592 | 0.018 | 2.612 | 13.628 | 4.343–42.758 |
|
|
| 1.182 | 3.260 | 1.051–10.108 | 0.041 | 0.645 | 1.907 | 0.635–5.727 | 0.250 |
|
| 2.185 | 8.888 | 1.054–74.996 | 0.045 | 1.208 | 3.449 | 0.805–2.874 | 0.371 |
OR, odds ratio; CI, confidence interval.Significant difference (p < 0.05) is highlighted by bold.