Systems biology of interstitial lung diseases: integration of mRNA and microRNA expression changes

Cho, Ji-Hoon; Gelinas, Richard; Wang, Kai; Etheridge, Alton; Piper, Melissa G; Batte, Kara; Dakhlallah, Duaa; Price, Jennifer; Bornman, Dan; Zhang, Shile; Marsh, Clay; Galas, David

doi:10.1186/1755-8794-4-8

BMC Medical Genomics

Table 3 Pathways associated with different network modules.

From: Systems biology of interstitial lung diseases: integration of mRNA and microRNA expression changes

			Module
		KEGG Pathway	1	2	3	4	5	6	7
Metabolism	Amino Acid Metabolism	Cysteine and methionine metabolism	7E-02
		Glycine, serine and threonine metabolism	5E-02
		Valine, leucine and isoleucine degradation	8E-03
	Biosynthesis of Secondary Metabolites	Terpenoid backbone biosynthesis	8E-03
	Carbohydrate Metabolism	Butanoate metabolism	7E-02
		Inositol phosphate metabolism		1E-02
		Propanoate metabolism	7E-02
		Pyruvate metabolism	3E-02
	Energy Metabolism	Reductive carboxylate cycle (CO2 fixation)	3E-02
	Glycan Biosynthesis and Metabolism	Glycosaminoglycan degradation	2E-03
		Glycosphingolipid biosynthesis - ganglio series	7E-02
		Heparan sulfate biosynthesis	4E-02
	Lipid Metabolism	Arachidonic acid metabolism	2E-02
		Ether lipid metabolism	8E-02
		Fatty acid elongation in mitochondria	2E-02
		Fatty acid metabolism	3E-02
		Glycerolipid metabolism	2E-03
		Glycerophospholipid metabolism	1E-02
		Sphingolipid metabolism			2E-02
		Steroid biosynthesis			*8E-05*
		Synthesis and degradation of ketone bodies	3E-02
	Metabolism of Cofactors and Vitamins	Nicotinate and nicotinamide metabolism	5E-04
		One carbon pool by folate	7E-02
	Metabolism of Other Amino Acids	Selenoamino acid metabolism	4E-02
	Xenobiotics Biodegradation and Metabolism	Benzoate degradation via CoA ligation	6E-02
		Caprolactam degradation	8E-03
Genetic Information Processing	Folding, Sorting and Degradation	RNA degradation					2E-02
Environmental Information Processing	Signal Transduction	ErbB signaling pathway		2E-02
		Hedgehog signaling pathway		*4E-05*
		Jak-STAT signaling pathway							1E-02
		MAPK signaling pathway		8E-02		5E-03	2E-03
		mTOR signaling pathway		1E-02
		Notch signaling pathway						4E-03
		Phosphatidylinositol signaling system		4E-02
		TGF-beta signaling pathway					4E-02	1E-02
		VEGF signaling pathway	6E-02	9E-03
		Wnt signaling pathway		1E-02				1E-04
	Signaling Molecules and Interaction	Cell adhesion molecules (CAMs)						3E-02
		Cytokine-cytokine receptor interaction		4E-03					6E-02
		ECM-receptor interaction	1E-02
Cellular Processes	Cell Communication	Adherens junction							3E-02
		Focal adhesion	1E-02	5E-04					3E-02
		Tight junction		4E-04
	Cell Growth and Death	Apoptosis		2E-02
		Cell cycle					8E-02
		p53 signaling pathway		3E-02
	Cell Motility	Regulation of actin cytoskeleton		9E-04
	Circulatory System	Vascular smooth muscle contraction	*4E-06*
	Development	Axon guidance		7E-02					7E-02
	Endocrine System	Adipocytokine signaling pathway		3E-02					*2E-06*
		GnRH signaling pathway		9E-02
		Insulin signaling pathway		*2E-05*			1E-02		*7E-05*
	Immune System	Antigen processing and presentation			8E-02
		B cell receptor signaling pathway		8E-03
		Chemokine signaling pathway		*2E-09*
		Complement and coagulation cascades	1E-02
		Fc epsilon RI signaling pathway		4E-02
		Fc gamma R-mediated phagocytosis		1E-03
		Leukocyte transendothelial migration		1E-02
		T cell receptor signaling pathway		2E-03
		Toll-like receptor signaling pathway	2E-02	9E-02
	Nervous System	Neurotrophin signaling pathway		*7E-06*
	Transport and Catabolism	Endocytosis		3E-04
Human Diseases	Cancers	Acute myeloid leukemia					2E-02
		Basal cell carcinoma		*3E-05*
		Chronic myeloid leukemia		8E-03				9E-03
		Colorectal cancer		1E-02			4E-02		3E-02
		Endometrial cancer		6E-02			1E-02
		Glioma		1E-01
		Pancreatic cancer		3E-02
		Pathways in cancer		*3E-07*				3E-03
		Prostate cancer					4E-02
		Renal cell carcinoma		3E-02
		Small cell lung cancer		1E-02
		Thyroid cancer					5E-03
	Circulatory Diseases	Arrhythmogenic right ventricular cardiomyopathy (ARVC)	6E-02
		Hypertrophic cardiomyopathy (HCM)							2E-04
	Infectious Diseases	Epithelial cell signaling in Helicobacter pylori infection		*2E-05*
	Neurodegenerative Diseases	Amyotrophic lateral sclerosis (ALS)		6E-02

With genes in each module of the network, pathway enrichment analysis was performed using one-sided Fisher exact test. The significance level of p-value is represented by regular (0.01~0.1), bold (0.0001~0.01) and bold-italic (<0.0001) fonts.

Back to article page

ISSN: 1755-8794

Contact us

Submission enquiries: bmcmedicalgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com