TABLE 2.

NETWORKS ASSOCIATED WITH DIFFERENTIALLY EXPRESSED GENES IN IDIOPATHIC PULMONARY FIBROSIS VERSUS NORMAL TISSUE

Score	Focus Molecules*	Top Functions
42	25	Connective tissue disorders, genetic disorder, dermatological diseases and conditions
36	23	Inflammatory response, gene expression, cell-to-cell signaling and interaction
35	22	Cellular compromise, inflammatory response, cellular function and maintenance
33	22	Cell-to-cell signaling and interaction, cellular movement, immune cell trafficking
31	20	Hematological disease, cancer, reproductive system disease
29	19	Inflammatory response, cellular movement, hematopoiesis
28	19	Inflammatory response, cardiovascular disease, lipid metabolism
23	17	Gene expression, cell death, cell cycle
23	16	Embryonic development, tissue development, nervous system development and function
21	17	Cell death, liver necrosis/cell death, organ morphology
21	15	Cell morphology, carbohydrate metabolism, developmental disorder
20	16	Cardiovascular disease, cell death, gastrointestinal disease
20	15	Cell-to-cell signaling and interaction, cellular assembly and organization, cellular development
19	15	Cell cycle, lipid metabolism, nervous system development and function
19	15	Antigen presentation, cellular movement, hematological system development and function

^*For a list of molecules, see Table E5. The genes used in the network analysis were selected on the basis of a false positive discovery rate (FDR). Because the genes with a fold change greater than 2 and a P value not greater than 0.05 had an FDR not exceeding 0.061, therefore all genes with a fold change greater than 2 and a P value not greater than 0.05 were used in the network analysis (see the online supplement for detail).