A network-based pathway-expanding approach for pathway analysis

BMC Bioinformatics

Table 1 Top 15 pathways identified from BRCA

Rank	Entry	Name	Score	SPIA	GSEA	Proof
1	hsa00750	Vitamin B6 metabolism	0.997735	No	No	[30–33]
2	hsa00072	Synthesis and degradation of ketone bodies	0.940425	No	Yes	[34–37]
3	hsa04122	Sulphur relay system	0.855753	No	No	[38, 39]
4	hsa00400	Phenylalanine,tyrosine and tryptophan biosynthesis	0.850563	No	No	[40]
5	hsa00533	Glycosaminoglycan biosynthesis	0.836469	No	No	[41–43]
6	hsa04964	Proximal tubule bicarbonate reclamation	0.803311	No	Yes	[46]
7	hsa01040	Biosynthesis of unsaturated fatty acids	0.799334	No	No	[47]
8	hsa00630	Glyoxylate and dicarboxylate metabolism	0.785954	No	Yes	[48]
9	hsa05217	Basal cell carcinoma	0.779876	No	No	[49, 50]
10	hsa00910	Nitrogen metabolism	0.77962	No	Yes	[51, 52]
11	hsa05218	Melanoma	0.758975	Yes	Yes	[53]
12	hsa04972	Pancreatic secretion	0.754263	No	Yes	[54, 55]
13	hsa00670	One carbon pool by folate	0.7452	No	No	[56]
14	hsa00900	Terpenoid backbone biosynthesis	0.736641	No	No	[57, 58]
15	hsa00920	Sulphur metabolism	0.733627	No	No	[59]

Note: Yes if the pathway was also ranked in the SPIA or GSEA top 15; No if otherwise

ISSN: 1471-2105