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Neuropsychiatric Disease and Treatment Volume 14, 2018 - Issue
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Original Research

Aberrantly expressed long noncoding RNAs and genes in Parkinson’s disease

Yong ZhouDepartment of Neurology, The Second Affiliated Hospital of Nantong University, The First People’s Hospital of Nantong, Nantong, China, [email protected]
,
Chengzhi GuDepartment of Neurology, The Second Affiliated Hospital of Nantong University, The First People’s Hospital of Nantong, Nantong, China, [email protected]
,
Jia LiDepartment of Neurology, The Second Affiliated Hospital of Nantong University, The First People’s Hospital of Nantong, Nantong, China, [email protected]
,
Lianhai ZhuDepartment of Neurology, The Second Affiliated Hospital of Nantong University, The First People’s Hospital of Nantong, Nantong, China, [email protected]
,
Guoxiang HuangDepartment of Neurology, The Second Affiliated Hospital of Nantong University, The First People’s Hospital of Nantong, Nantong, China, [email protected]
,
Jie DaiDepartment of Neurology, The Second Affiliated Hospital of Nantong University, The First People’s Hospital of Nantong, Nantong, China, [email protected]
&
Huaiyu HuangDepartment of Neurology, The Second Affiliated Hospital of Nantong University, The First People’s Hospital of Nantong, Nantong, China, [email protected]Correspondence[email protected]
 show all
Pages 3219-3229 | Published online: 22 Nov 2018

Figures & data

Table 1 Top ten up- and downregulated DElncRNAs between PD and normal controls

Table 2 Top ten up- and downregulated DEmRNAs between PD and normal controls

Figure 1 DElncRNAs and DEmRNAs between PD and normal controls.

Notes: (A, B) Hierarchical clustering results of DElncRNAs and top 100 DEmRNAs between PD and normal controls, respectively. Row and column represent DElncRNAs/DEmRNAs and tissue samples, respectively. The color scale represents the expression levels. (C) Distribution of DElncRNAs and DEmRNAs on chromosomes. The outer layer cycle was the chromosome map of the human genome hg19 (GRCh37). The red and blue inner layer represents the distribution of up- and downregulated DEmRNAs on different chromosomes, respectively. The pink and light blue inner layer represents the distribution of up- and downregulated DElncRNAs on different chromosome, respectively.
Abbreviations: DElncRNAs, differentially expressed long noncoding RNAs; DEmRNAs, differentially expressed micro RNAs; PD, Parkinson’s disease.
Figure 1 DElncRNAs and DEmRNAs between PD and normal controls.

Figure 2 Significantly enriched GO terms and KEGG pathways of DEmRNAs between PD and normal controls.

Notes: (A) BP, (B) CC, (C) MF, and (D) KEGG pathways. The x-axis shows counts of DEmRNAs enriched in GO terms or KEGG pathways and the y-axis shows GO terms or KEGG pathways. The color scale represented −log FDR.
Abbreviations: BP, biological process; CC, cellular component; DEmRNAs, differentially expressed mRNAs; FDR, false discovery rate; GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MF, molecular function.
Figure 2 Significantly enriched GO terms and KEGG pathways of DEmRNAs between PD and normal controls.

Figure 3 PD-specific PPI network.

Notes: The red and blue ellipses represent proteins encoded by up- and downregulated DEmRNAs between PD and normal control. Ellipses with black and blue border are DEmRNAs derived from top ten down- and upregulated DEmRNAs between PD and normal control.
Abbreviations: DEmRNAs, differentially expressed mRNAs; PD, Parkinson’s disease; PPI, protein–protein interaction.
Figure 3 PD-specific PPI network.

Table 3 Nearby targeted DEmRNAs of DElncRNAs between PD and normal controls

Figure 4 Validation of selected DEmRNAs in GSE57475.

Notes: The x-axis shows PD and normal control groups and the y-axis shows relative expression levels. (A) TAL1; (B) TREML1; (C) TREML4; (D) ERBB2; (E) CX3CR1; (F) ANK1. The circles represent outliers.
Abbreviations: DEmRNAs, differentially expressed micro RNAs; PD, Parkinson’s disease.
Figure 4 Validation of selected DEmRNAs in GSE57475.

Figure 5 Validation of selected DEmRNAs in GSE68719.

Notes: The x-axis shows PD and normal control groups and the y-axis shows relative expression levels. (A) TAL1; (B) TREML1; (C) ERBB2; (D) CX3CR1; (E) ANK1; (F) KLRD1. The circles represent outliers. *P < 0.05 and **P < 0.01.
Abbreviations: DEmRNAs, differentially expressed micro RNAs; PD, Parkinson’s disease.
Figure 5 Validation of selected DEmRNAs in GSE68719.
Figure 5 Validation of selected DEmRNAs in GSE68719.

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