Table 6.
Statistical summary of the gene set enrichment analysis of the lipid metabolism genes in the SN and putamen from PD patients and controls.
| Name | Source | NGenes | Direction | p Value | FDR | p Value.Mixed | FDR.Mixed |
|---|---|---|---|---|---|---|---|
| SN | |||||||
| Phosphatidylcholines | GeneRIF Biological Term Annotations | 5 | Up | 0.034 | 0.246 | 0.095 | 0.151 |
| Phosphatidylcholine Biosynthesis | HumanCyc Pathways | 6 | Down | 0.070 | 0.246 | 0.114 | 0.151 |
| Phosphatidylcholine | Human Metabolome Database | 81 | Up | 0.074 | 0.246 | 0.124 | 0.151 |
| Phosphatidylcholines | CTD Gene-Chemical Interactions | 36 | Up | 0.084 | 0.246 | 0.189 | 0.206 |
| Phosphatidylcholines | dbGAP Gene-Trait Associations | 3 | Up | 0.124 | 0.246 | 0.126 | 0.151 |
| Phosphatidylcholine Biosynthesis Pathway | Biocarta Pathways | 3 | Down | 0.134 | 0.246 | 0.056 | 0.151 |
| GO:0031210 | phosphatidylcholine binding | 30 | Up | 0.144 | 0.246 | 0.111 | 0.151 |
| GO:0046470 | phosphatidylcholine metabolic process | 14 | Up | 0.414 | 0.622 | 0.060 | 0.151 |
| Phosphatidylcholinespecific | GeneRIF Biological Term Annotations | 5 | Up | 0.693 | 0.866 | 0.538 | 0.538 |
| GO:0034638 | phosphatidylcholine catabolic process | 5 | Up | 0.734 | 0.866 | 0.026 | 0.151 |
| GO:0006656 | phosphatidylcholine biosynthetic process | 45 | Down | 0.794 | 0.866 | 0.025 | 0.151 |
| Phosphatidylcholine | GeneRIF Biological Term Annotations | 31 | Down | 0.949 | 0.949 | 0.123 | 0.151 |
| GO:0008429 | phosphatidylethanolamine binding | 11 | Up | 0.096 | 0.390 | 0.254 | 0.355 |
| Phosphatidylethanolamine | CTD Gene-Chemical Interactions | 4 | Up | 0.130 | 0.390 | 0.480 | 0.480 |
| Phosphatidylethanolamine | Human Metabolome Database | 45 | Up | 0.344 | 0.687 | 0.272 | 0.355 |
| GO:0006646 | phosphatidylethanolamine biosynthetic process | 15 | Down | 0.577 | 0.704 | 0.025 | 0.120 |
| Phosphatidylethanolamine Biosynthesis | HumanCyc Pathways | 5 | Down | 0.587 | 0.704 | 0.040 | 0.120 |
| Phosphatidylethanolamine | GeneRIF Biological Term Annotations | 13 | Up | 0.822 | 0.822 | 0.296 | 0.355 |
| GO:0001786 | phosphatidylserine binding | 58 | Up | 0.046 | 0.457 | 0.064 | 0.214 |
| Phosphatidylserines | CTD Gene-Chemical Interactions | 9 | Up | 0.104 | 0.519 | 0.483 | 0.591 |
| Phosphatidylserineexpressing | GeneRIF Biological Term Annotations | 4 | Up | 0.308 | 0.955 | 0.532 | 0.591 |
| Phosphatidylserine | DrugBank Drug Targets | 10 | Up | 0.416 | 0.955 | 0.059 | 0.214 |
| Phosphatidylserine | GeneRIF Biological Term Annotations | 75 | Up | 0.611 | 0.955 | 0.202 | 0.337 |
| GO:0006659 | phosphatidylserine biosynthetic process | 5 | Down | 0.752 | 0.955 | 0.125 | 0.256 |
| GO:0006658 | phosphatidylserine metabolic process | 5 | Down | 0.777 | 0.955 | 0.514 | 0.591 |
| Phosphatidylserine | Human Metabolome Database | 45 | Up | 0.816 | 0.955 | 0.128 | 0.256 |
| GO:0006660 | phosphatidylserine catabolic process | 8 | Up | 0.940 | 0.955 | 0.006 | 0.060 |
| Phosphatidylserinebinding | GeneRIF Biological Term Annotations | 3 | Up | 0.955 | 0.955 | 0.988 | 0.988 |
| Phosphatidylinositolbinding | GeneRIF Biological Term Annotations | 4 | Up | 0.032 | 0.380 | 0.521 | 0.556 |
| Phosphatidylinositols | CTD Gene-Chemical Interactions | 17 | Up | 0.134 | 0.493 | 0.052 | 0.304 |
| Phosphatidylinositol4 | GeneRIF Biological Term Annotations | 3 | Up | 0.158 | 0.493 | 0.166 | 0.304 |
| GO:0035091 | phosphatidylinositol binding | 99 | Down | 0.164 | 0.493 | 0.174 | 0.304 |
| Phosphatidylinositol Signaling System | KEGG Pathways | 72 | Up | 0.344 | 0.675 | 0.406 | 0.541 |
| Phosphatidylinositol | GeneRIF Biological Term Annotations | 331 | Up | 0.407 | 0.675 | 0.105 | 0.304 |
| GO:0046488 | phosphatidylinositol metabolic process | 24 | Up | 0.479 | 0.675 | 0.203 | 0.304 |
| GO:0006661 | phosphatidylinositol biosynthetic process | 78 | Up | 0.559 | 0.675 | 0.198 | 0.304 |
| GO:0046854 | phosphatidylinositol phosphorylation | 53 | Down | 0.641 | 0.675 | 0.147 | 0.304 |
| GO:0046856 | phosphatidylinositol dephosphorylation | 23 | Up | 0.648 | 0.675 | 0.557 | 0.557 |
| Phosphatidylinositol3 | GeneRIF Biological Term Annotations | 24 | Down | 0.655 | 0.675 | 0.523 | 0.556 |
| Phosphatidylinositol | Human Metabolome Database | 85 | Up | 0.676 | 0.676 | 0.183 | 0.304 |
| Putamen | |||||||
| GO:0035091 | phosphatidylinositol binding | 99 | Down | 0.010 | 0.124 | 0.500 | 0.883 |
| Phosphatidylinositols | CTD Gene-Chemical Interactions | 17 | Up | 0.049 | 0.296 | 0.279 | 0.883 |
| Phosphatidylinositol | Human Metabolome Database | 85 | Down | 0.179 | 0.715 | 0.813 | 0.883 |
| GO:0046854 | phosphatidylinositol phosphorylation | 53 | Down | 0.624 | 0.981 | 0.582 | 0.883 |
| GO:0046856 | phosphatidylinositol dephosphorylation | 23 | Down | 0.723 | 0.981 | 0.883 | 0.883 |
| GO:0046488 | phosphatidylinositol metabolic process | 24 | Down | 0.727 | 0.981 | 0.710 | 0.883 |
| Phosphatidylinositolbinding | GeneRIF Biological Term Annotations | 78 | Down | 0.748 | 0.981 | 0.726 | 0.883 |
| GO:0006661 | phosphatidylinositol biosynthetic process | 4 | Down | 0.756 | 0.981 | 0.645 | 0.883 |
| Phosphatidylinositol3 | GeneRIF Biological Term Annotations | 24 | Down | 0.759 | 0.981 | 0.749 | 0.883 |
| Phosphatidylinositol | GeneRIF Biological Term Annotations | 331 | Down | 0.919 | 0.981 | 0.495 | 0.883 |
| Phosphatidylinositol4 | GeneRIF Biological Term Annotations | 3 | Up | 0.975 | 0.981 | 0.410 | 0.883 |
| Phosphatidylinositol Signaling System | KEGG Pathways | 72 | Down | 0.981 | 0.981 | 0.631 | 0.883 |
| Sphingomyelin Metabolism/Ceramide Salvage | HumanCyc Pathways | 8 | Down | 0.028 | 0.220 | 0.104 | 0.623 |
| Sphingomyelins | dbGAP Gene-Trait Associations | 3 | Up | 0.134 | 0.393 | 0.402 | 0.623 |
| GO:0006685 | sphingomyelin catabolic process | 7 | Down | 0.147 | 0.393 | 0.167 | 0.623 |
| Sphingomyelin | Human Metabolome Database | 52 | Down | 0.232 | 0.464 | 0.764 | 0.764 |
| Sphingomyelins | CTD Gene-Chemical Interactions | 4 | Down | 0.334 | 0.535 | 0.467 | 0.623 |
| GO:0006686 | sphingomyelin biosynthetic process | 6 | Down | 0.443 | 0.590 | 0.291 | 0.623 |
| GO:0006684 | sphingomyelin metabolic process | 4 | Down | 0.556 | 0.635 | 0.716 | 0.764 |
| Sphingomyelin | GeneRIF Biological Term Annotations | 29 | Up | 0.900 | 0.900 | 0.339 | 0.623 |
Summary of results for the gene set enrichment tests of lipid metabolism genes. The table depicts the name of the pathway (Name), its source (Source) and the number of transcripts present in our dataset (NGenes). The results are shown with the controls (i.e., ‘Up’ refers to the gene set being increased in Parkinson’s disease (PD) patients compared to controls, and ‘Down’ the opposite). The hypothesis of ‘Mixed’ refers to the gene set including DEGs in both directions. FDR, false discovery rate; Mixed, non-directional analysis.