TABLE VII.

The resulting ranks and p-values for all the pathways from analyzing the data set that studies alzheimer disease [6] that have FDR-corrected p-value lower than 5%. We studied the association of these top pathways to alzheimer disease. The pathway shown in red is the target pathway with the name corresponding to the disease under study. The bold pathways are the ones with known association with alzheimer disease based on existing literature. The number of bold and red pathways represents the number of true positives found by the method. Here we can see 16 true positives with FDR-corrected p-value lower than 5%.

	Name	ID	p-values	FDR	ranks	references
1	Alzheimer’s disease	05010	5e-06	5e-05	4.74
2	Cytokine-cytokine receptor interaction	04060	5e-06	5e-05	4.74	[39]
3	Glutamatergic synapse	04724	5e-06	5e-05	4.74	[11]
4	GABAergic synapse	04727	5e-06	5e-05	4.74	[28]
5	Dopaminergic synapse	04728	5e-06	5e-05	4.74	[30]
6	Long-term depression	04730	5e-06	5e-05	4.74	[37]
7	Endocrine and other factor-regulated calcium reabsorption	04961	5e-06	5e-05	4.74
8	Parkinson’s disease	05012	5e-06	5e-05	4.74	[2], [8]
9	Amyotrophic lateral sclerosis (ALS)	05014	5e-06	5e-05	4.74	[31]
10	Huntington’s disease	05016	5e-06	5e-05	4.74	[12], [8]
11	Vibrio cholerae infection	05110	5e-06	5e-05	4.74
12	Pathogenic Escherichia coli infection	05130	5e-06	5e-05	4.74
13	Oocyte meiosis	04114	1e-03	0.01	10.95
14	Long-term potentiation	04720	1e-03	0.01	10.95	[51], [25]
15	Retrograde endocannabinoid signaling	04723	1e-03	0.01	10.95	[33]
16	Gastric acid secretion	04971	1e-03	0.01	10.95
17	Pancreatic secretion	04972	1e-03	0.01	10.95
18	VEGF signaling pathway	04370	2e-03	0.01	13.87	[38], [14]
19	Epithelial cell signaling in Helicobacter pylori infection	05120	2e-03	0.01	13.87
20	Systemic lupus erythematosus	05322	2e-03	0.01	13.87
21	Salmonella infection	05132	3e-03	0.02	15.33
22	Calcium signaling pathway	04020	0.01	0.03	16.79	[59], [7]
23	Salivary secretion	04970	0.01	0.03	16.79
24	Arrhythmogenic right ventricular cardiomyopathy (ARVC)	05412	0.01	0.03	16.79
25	Gap junction	04540	0.01	0.03	18.25	[29], [46]
26	Phosphatidylinositol signaling system	04070	0.01	0.04	18.98	[62], [4]
27	Morphine addiction	05032	0.01	0.04	19.71
28	Protein processing in endoplasmic reticulum	04141	0.01	0.04	20.80	[53]
29	Shigellosis	05131	0.01	0.04	20.80
30	Renal cell carcinoma	05211	0.01	0.05	21.90