Identification of functional modules that correlate with phenotypic difference: the influence of network topology

Table 4 Pathways from the small cell lung cancer dataset found exclusively by PWEA

Pathway	Size	DE fraction^a	Type	Possible relation to the cancer	Reference
GnRH signaling pathway	78	37%	Endocrine system	Negative autocrine regulator	[43, 79]
Complement and coagulation cascades	56	54%	Immune system	Inflammation Metastatic and invasive properties	[80]
MAPK signaling pathway	199	38%	Signal transduction	Cell growth	-
Fc epsilon RI signaling pathway	63	44%	Immune system	Angiogenesis Inflammation	[37, 41, 42]
Apoptosis	67	34%	Cell growth and death	Apoptosis	-
ABC transporters	34	24%	Membrane transport	Drug resistance	[81]
Jak-STAT signaling pathway	93	37%	Signal transduction	Cell growth	[47–49]
Drug metabolism - cytochrome P450	41	51%	Xenobiotics biodegradation and metabolism	Anticancer drugs topotecan and etoposide	[75]
Drug metabolism - other enzymes	28	46%	Xenobiotics biodegradation and metabolism	Anticancer drug irinotecan	[75]
Histidine metabolism	24	42%	Amino acid metabolism	Nutrition intake. Small cell lung cancer marker, DDC involved.	[82, 83]
Tryptophan metabolism	36	39%	Amino acid metabolism	As above	[82, 83]
Phenylalanine metabolism	13	54%	Amino acid metabolism	As above	[82, 83]
Fatty acid metabolism	37	38%	Lipid metabolism	Apoptosis. Therapeutic target	[84, 85]
Basal cell carcinoma	36	17%	Disease	Proliferation invasion through hedgehog signaling pathway	-

^aDE fraction is the fraction of genes that show differential expression with P < 0.05 using a two-tailed t-test. DDC: enzymatic neuroendocrine markers L-DOPA decarboxylase.

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