Table 1. Pathways enriched between 6 h and 72 h of FD induction.
Mean Normalised Enrichment Score (NES) and false discovery rate (FDR) for the biological pathways identified by GSEA in FD induction. Most genes responding to FD are involved in mitochondrial energy metabolism. The NES reflects the degree to which a set of genes is over-represented at either the top or bottom of a ranked list of genes while also taking into account differences in pathway size (i.e. gene-set size) and is the primary statistic for examining enrichment results, and for comparing results across pathways.
| Pathway | Core genes | Database | NES | FDR |
|---|---|---|---|---|
| Huntingtons disease | APAF1, ATP5C1, ATP5D, ATP5E, ATP5F1, ATP5H, ATP5O, BDNF, CASP3, CASP8, CLTA, COX4I1, COX5A, COX6A1, COX6C, COX7A2, COX7A2L, COX7C, COX8A, CYCS, DNAH3, DNAI1, DNAL1, DNALI1, GPX1, HDAC2, IFT57, NDUFA1, NDUFA10, NDUFA2, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFB1, NDUFB10, NDUFB3, NDUFB4, NDUFB5, NDUFB6, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV3, PLCB1, PLCB4, POLR2D, POLR2F, POLR2J, POLR2L, PPID, SDHA, SLC25A4, SLC25A6, SOD2, TAF4, TBP, TBPL1, TFAM, UQCR10, UQCR11, UQCRFS1, UQCRH, VDAC3 | KEGG | 1.76 | 0.15 |
| Oxidative phosphorylation | ATP5C1, ATP5D, ATP5E, ATP5F1, ATP5H, ATP5I, ATP5J2, ATP5O, ATP6V0D2, ATP6V1G1, COX11, COX15, COX17, COX4I1, COX5A, COX6A1, COX6C, COX7A2, COX7A2L, COX7C, COX8A, NDUFA1, NDUFA10, NDUFA2, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFB1, NDUFB10, NDUFB3, NDUFB4, NDUFB5, NDUFB6, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV3, PPA1, PPA2, SDHA, UQCR10, UQCR11, UQCRFS1, UQCRH | KEGG | 1.81 | 0.16 |
| Mitochondrial protein import | BCS1L, CHCHD4, COX17, DNAJC19, GRPEL1, HSCB, HSPD1, PAM16, PMPCA, PMPCB, SAMM50, SLC25A12, SLC25A4, SLC25A6, TIMM13, TIMM17A, TIMM22, TIMM44, TIMM9, TOMM22, TOMM5, TOMM7 | Reactome | 1.80 | 0.16 |
| One carbon pool by folate | ATIC, DHFR, GART, MTFMT, MTHFD1, MTHFD1L, MTHFS, TYMS | KEGG | 1.74 | 0.17 |
| Cholesterol biosynthesis | DHCR7, FDFT1, GGPS1, HMGCR, HMGCS1, IDI1, MSMO1, NSDHL, SQLE | Reactome | 1.77 | 0.17 |
| Antigen processing cross presentation | CD36, CTSS, NCF4, PSMA1, PSMA2, PSMA3, PSMA5, PSMA6, PSMA7, PSMB1, PSMB2, PSMB3, PSMC1, PSMC2, PSMC3, PSMC5, PSMD1, PSMD10, PSMD3, PSMD5, RPS27A, SEC61B, SEC61G, TAP1, UBA52 | Reactome | 1.74 | 0.18 |
| Alzheimers disease | NDUFB6, CYCS, NDUFB3, NDUFA8, UQCR11, NDUFC2, ATP5F1, ATP5E, NDUFB5, UQCR10, COX4I1, COX6A1, COX7C, NDUFB10, NDUFB1, CASP8, NDUFV3, NDUFA6, ATP5H, COX7A2, RYR3, NDUFA2, NDUFC1, NDUFS1, NDUFA1, SDHA, NDUFB8, NDUFA4, NDUFA5, APAF1, UQCRH, ATP5O, NDUFA7, NDUFS6, NDUFS4, ATP5D, ATP5C1, NDUFB9, CACNA1D, NDUFS8, NDUFS3, NDUFS7, CASP3, COX8A, COX6C, COX5A, NDUFA10, ATP2A1, COX7A2L, TNFRSF1A, UQCRFS1, PSEN1, NDUFB4, IL1B, PLCB1, NCSTN, PLCB4 | KEGG | 1.74 | 0.19 |
| Parkinsons disease | APAF1, ATP5C1, ATP5D, ATP5E, ATP5F1, ATP5H, ATP5O, CASP3, COX4I1, COX5A, COX6A1, COX6C, COX7A2, COX7A2L, COX7C, COX8A, CYCS, GPR37, NDUFA1, NDUFA10, NDUFA2, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFB1, NDUFB10, NDUFB3, NDUFB5, NDUFB6, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV3, PARK7, PPID, SDHA, SLC25A4, SNCAIP, UBE2L3, UQCR10, UQCR11, UQCRH, VDAC3 | KEGG | 1.77 | 0.19 |
| TCA cycle and respiratory electron transport | ATP5C1, ATP5D, ATP5E, ATP5F1, ATP5H, ATP5I, ATP5J2, ATP5O, COX4I1, COX5A, COX6A1, COX6C, COX7A2L, COX7C, COX8A, CYCS, D2HGDH, DLD, IDH3A, LDHB, NDUFA1, NDUFA10, NDUFA2, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFB1, NDUFB10, NDUFB3, NDUFB5, NDUFB6, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV3, NNT, SDHA, SUCLG1, SUCLG2, UQCR11, UQCRH | Reactome | 1.72 | 0.19 |
| Respiratory electron transport | COX4I1, COX5A, COX6A1, COX6C, COX7A2L, COX7C, COX8A, CYCS, NDUFA1, NDUFA10, NDUFA12, NDUFA2, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFB1, NDUFB10, NDUFB3, NDUFB4, NDUFB5, NDUFB6, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV3, SDHA, UQCR11, UQCRFS1, UQCRH | Reactome | 1.81 | 0.21 |
| Respiratory electron transport ATP synthesis by chemiosmotic coupling and heat production by uncoupling proteins | ATP5C1, ATP5D, ATP5E, ATP5F1, ATP5H, ATP5I, ATP5J2, ATP5O, COX4I1, COX5A, COX6A1, COX6C, COX7A2L, COX7C, COX8A, CYCS, NDUFA1, NDUFA10, NDUFA12, NDUFA2, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFB1, NDUFB10, NDUFB3, NDUFB4, NDUFB5, NDUFB6, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS1, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV3, SDHA, UCP3, UQCR11, UQCRFS1, UQCRH | Reactome | 1.83 | 0.23 |
| Translation | EEF1B2, EIF2B1, EIF2B2, EIF2S1, EIF2S2, EIF2S3, EIF3D, EIF3H, EIF3I, EIF3J, EIF4EBP1, EIF4H, EIF5B, RPL10A, RPL11, RPL13, RPL14, RPL18A, RPL19, RPL21, RPL22, RPL23A, RPL24, RPL26L1, RPL27, RPL27A, RPL29, RPL30, RPL32, RPL35, RPL35A, RPL36, RPL36A, RPL37, RPL37A, RPL38, RPL39, RPL5, RPL6, RPL7, RPL8, RPLP1, RPLP2, RPN1, RPS10, RPS11, RPS14, RPS15, RPS15A, RPS16, RPS2, RPS20, RPS23, RPS24, RPS25, RPS26, RPS27A, RPS28, RPS29, RPS3, RPS3A, RPS4X, RPS6, RPS7, RPS8, RPSA, SEC61B, SEC61G, SPCS1, SPCS2, SPCS3, SRP19, SRP72, SSR3, UBA52 | Reactome | 1.69 | 0.24 |
| ER phagosome pathway | PSMA1, PSMA2, PSMA3, PSMA5, PSMA6, PSMA7, PSMB1, PSMB2, PSMB3, PSMC1, PSMC2, PSMC3, PSMC5, PSMD1, PSMD10, PSMD3, PSMD5, RPS27A, SEC61B, SEC61G, TAP1, UBA52 | Reactome | 1.67 | 0.25 |