Table 1.

Disease-specific mediating GO Biological Processes for each pulmonary disorder. Selected GO terms with p_cent < 0.01 (highlighted in bold) in exactly one of the pulmonary disorders. Full results are available in Supplementary Table S1. Colors indicate functional classes; immune: blue; oxygen/oxidative-stress response: green; signaling: yellow; neurodevelopment: orange; adhesion/ECM/structural: red; metabolic: pink; homeostasis: purple. An asterisk on the right (“Not HG”) means that neither that pathway nor any similar pathway is significantly enriched (with hypergeometric (HG) FDR < 0.05) in either the disease gene set or the differentially-expressed gene set for the indicated disease.

	Pathway	asthma p-value	BPD p-value	COPD p-value	Not HG
blue	Positive Regulation of Mast Cell Activation	0.0013	0.0651	0.2274
blue	Myeloid Cell Activation Involved in Immune Response	0.0016	0.1200	0.2881
blue	Leukocyte Degranulation	0.0075	0.1483	0.3737
blue	T Cell Mediated Immunity	0.0033	0.0613	0.9692
blue	Antigen Processing… via MHC class II	0.0050	0.0560	0.6590
blue	Positive Regulation of B Cell Differentiation	0.0068	0.0942	0.2204	*
blue	Macrophage Activation Involved in Immune Response	0.0077	0.0705	0.1990
green	Cation Transport	0.0004	0.1773	0.1186
green	Positive Regulation of Calcium Mediated Signaling	0.0052	0.0541	0.4756
green	Positive Regulation of Nitric Oxide Synthase Activity	0.0053	0.1376	0.1330
yellow	Positive Regulation of ERBB Signaling Pathway	0.0030	0.1172	0.2060	*
red	Positive Regulation of Cell Adhesion Mediated by Integrin	0.0080	0.0743	0.3015
pink	Amyloid Precursor Protein Metabolic Process	0.0027	0.8259	0.7919	*
pink	Regulation of Glucose Import	0.0044	0.0944	0.2334
blue	Negative Regulation of TNF Mediated Signaling Pathway	0.3954	0.0042	0.1453
blue	Negative Regulation of Antigen Receptor Mediated Signaling	0.2772	0.0004	0.2115	*
blue	Negative Regulation of T Cell Receptor Signaling Pathway	0.2701	0.0005	0.2132	*
blue	B Cell Mediated Immunity	0.1489	0.0006	0.0667	*
blue	Regulation of Interleukin 1 Secretion	0.4228	0.0083	0.4387
yellow	Epidermal Growth Factor Receptor Signaling Pathway	0.1158	0.0000	0.1275	*
yellow	Regulation of Insulin Like Growth Factor Receptor Signaling	0.4711	0.0002	0.1137	*
yellow	Activation of MAPKK Activity	0.1732	0.0033	0.4494	*
yellow	VEGF Receptor Signaling Pathway	0.1577	0.0063	0.0732	*
orange	Forebrain Development	0.3310	0.0000	0.1579	*
orange	Cerebral Cortex Cell Migration	0.3632	0.0016	0.9484	*
orange	Neuroepithelial Cell Differentiation	0.0947	0.0031	0.9680	*
orange	Auditory Receptor Cell Differentiation	0.0814	0.0008	0.8433	*
red	Positive Reg. of Substrate Adhesion Dependent Cell Spreading	0.4722	0.0005	0.0626	*
red	Actin Filament Organization	0.1692	0.0034	0.1645
red	Wound Healing	0.0665	0.0002	0.1049
pink	Regulation of Glucose Metabolic Process	0.5563	0.0041	0.2729	*
pink	Positive Regulation of Phospholipid Metabolic Process	0.1055	0.0006	0.1371
blue	Negative Regulation of TGF Beta Receptor Signaling Pathway	0.1454	0.1127	0.0001
blue	Positive Regulation of Adaptive Immune Response	0.2672	0.2108	0.0004
blue	Positive Regulation of Natural Killer Cell Activation	0.3802	0.1776	0.0026	*
blue	Negative Regulation of Leukocyte Migration	0.1067	0.2482	0.0038
green	Response to Metal Ion	0.0588	0.0729	0.0000
green	Reactive Oxygen Species Metabolic Process	0.1188	0.1878	0.0003
green	Response to Increased Oxygen Levels	0.6638	0.2764	0.0034
green	Negative Regulation of Apoptotic Signaling Pathway	0.3339	0.1617	0.0023
red	Regulation of Extracellular Matrix Organization	0.1161	0.0692	0.0006
pink	Regulation of Amyloid Precursor Protein Catabolic Process	0.1834	0.1097	0.0038	*
violet	Lipid Homeostasis	0.5030	0.1191	0.0000	*
violet	Anion Homeostasis	0.3261	0.0796	0.0022
violet	Acylglycerol Homeostasis	0.6552	0.1044	0.0033	*