Table 2.
Summary of publicly available transcriptomic studies on human postmortem substantia nigra (SN) and/or putamen from PD patients and controls.
| Accession Number | Tissue | Control | PD Patient | Platform | Inclusion |
|---|---|---|---|---|---|
| GSE7621 | SN | 9 | 16 | [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array | Yes |
| GSE42966 | SN | 6 | 9 | Agilent-014850 Whole Human Genome Microarray 4x44K G4112F | Yes |
| GSE43490 | SN | 5 | 8 | Agilent-014850 Whole Human Genome Microarray 4x44K G4112F | No (only overexpressed genes) |
| GSE49036 | SN | 8 | 15 | [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array | Yes |
| GSE20164 | SN | 5 | 6 | [HG-U133A] Affymetrix Human Genome U133A Array | Yes |
| GSE20163 | SN | 9 | 8 | [HG-U133A] Affymetrix Human Genome U133A Array | Yes |
| GSE20292 | SN | 18 | 11 | [HG-U133A] Affymetrix Human Genome U133A Array | No (no DEGs) |
| GSE20333 | SN | 6 | 6 | [HG-Focus] Affymetrix Human HG-Focus Target Array | Yes |
| GSE8397 | SNm | 7 | 9 | [HG-U133A] Affymetrix Human Genome U133A Array; [HG-U133B] Affymetrix Human Genome U133B Array | No (two different SN tissues (medial and lateral)) |
| SNl | 8 | 15 | |||
| GSE54282 | SN | 3 | 3 | [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZG_15.0.0] | Yes |
| Put | 6 | 6 | Yes | ||
| GSE77666 | Put | 12 | 12 | NanoString nCounter gene expression system | Yes |
| GSE23290 | Put | 5 | 5 | [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array | Yes |
| GSE20291 | Put | 20 | 15 | [HG-U133A] Affymetrix Human Genome U133A Array | No (no DEGs) |
Data includes GEO Data Sets accession number, tissue, number of controls and PD patients, platform used and inclusion or exclusion criteria. The analysis and visualization of functional profiles was done with clusterProfiler [35]. Finally, we performed protein–protein interaction network analysis of the common differentially expressed genes (DEGs) with STRING, using only the highest confidence interaction score [36].