A validated analysis pipeline for mass spectrometry-based vitreous proteomics: new insights into proliferative diabetic retinopathy

Table 3 iPathway guide results

Comparison Group	Pathway	Overrepresentation	Perturbation	DE Genes	All Genes	FDR-corrected ORA p-value
All PDR vs. All CTL	Metabolic pathways	Yes	No	52	83	1.24E−02
All PDR vs. All CTL	Carbon metabolism	Yes	No	16	19	1.93E−02
All PDR vs. All CTL	Glycolysis/gluconeogenesis	Yes	No	13	15	3.27E−02
PDR-L vs. CTL	Metabolic pathways	Yes	No	32	83	3.16E−02
PDR-L vs. CTL	Proteasome	Yes	No	6	7	3.16E−02
PDR-L vs. CTL	Platelet activation	Yes	Yes	7	9	3.16E−02
PDR-L vs. CTL	Glycolysis/gluconeogenesis	Yes	No	9	15	4.60E−02
PDR-L vs. CTL	HIF-1 signaling pathway	Yes	Yes	7	10	4.60E−02
PDR-M vs. CTL	Metabolic pathways	Yes	No	45	83	1.69E−03
PDR-M vs. CTL	Carbon metabolism	Yes	No	15	19	2.97E−03
PDR-M vs. CTL	Glycolysis/gluconeogenesis	Yes	No	12	15	1.11E−02
PDR-M vs. CTL	Pentose phosphate pathway	Yes	No	7	7	1.32E−02
PDR-M vs. CTL	Proteasome	Yes	No	7	7	1.32E−02
PDR-H vs. CTL	Metabolic pathways	Yes	No	57	83	3.48E−03
PDR-H vs. CTL	Carbon metabolism	Yes	No	17	19	1.19E−02

Pathway analysis results obtained using iPathway Guide (Advaita). All individually treated PDR samples were compared to all individually treated experiment 2 control samples (All PDR v.s All CTL). PDR subphenotypes were also compared to all control samples. CTL, control. DE, differentially expressed. ORA, overrepresentation analysis

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