PathNet: a tool for pathway analysis using topological information

Table 2 Pathways co-enriched with the AD pathway

Frequency	Pathway name	(KEGG ID)	References
6	*Bacterial invasion…	(5100)	[24]
6	*Regulation of actin…	(4810)	[25]
5	*Adherens junction	(4520)	[26]
5	*Focal adhesion	(4510)	[27–29]
5	*Huntington's disease	(5016)	[30]
5	*Long-term potenti…	(4720)	[31, 32]
5	*Parkinson's disease	(5012)	[30, 33]
5	Pathogenic Escher*…	(5130)	NA
4	Endocytosis	(4144)	[34]
4	Melanoma	(5218)	[35–37]
4	Pathways in cancer	(5200)	[35–37]
4	Shigellosis	(5131)	NA
3	ECM-receptor	(4512)	[38]
3	Endometrial cancer	(5213)	[35–37]
3	ErbB signaling	(4012)	[39]
3	Fc gamma R-	(4666)	[31]
3	Glioma	(5214)	[40]
3	MAPK signaling	(4010)	[41]
3	Phosphatidylinosit…	(4070)	[42, 43]
3	Progesterone-med…	(4914)	NA
3	Proteasome	(3050)	[44, 45]

List of pathways co-enriched with the Alzheimer’s disease (AD) pathway in the six out of nine comparisons (moderate and severe samples in the disease progression dataset; and primary visual cortex, hippocampal field CA1, middle temporal gyrus, and posterior cingulate cortex regions in the brain regions dataset) where the AD pathway is enriched. The ‘Frequency’ column shows the number of times the pathway was co-enriched. Pathways that are frequently co-enriched (frequency ≥ 5) are indicated by an asterisk (*). The ‘References’ column provides support for the association of each of these co-enriched pathways with AD. NA: not available.

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