Supplemental Table 4. GeneGo pathway maps obtained using ontology enrichment, proteins with differing patterns of overexpression (indicated by table headers), and mapping onto GeneGo pathway maps*

GeneGO process networks / O-E / O-L / PO-E / PO-L / O / PO / L / E
Niacin-HDL metabolism / 3.16E-05 / - / - / - / 5.01E-05 / - / - / 6.31E-05
Regulation of metabolism_Bile acids regulation of glucose and lipid metabolism via FXR / 1.00E-03 / - / - / - / 1.58E-03 / - / - / 2.00E-03
Regulation of lipid metabolism_Regulation of lipid metabolism by niacin and isoprenaline / 1.58E-03 / - / - / - / 2.51E-03 / - / - / 2.51E-03
Cell cycle_Nucleocytoplasmic transport of CDK/Cyclins / 2.00E-02 / - / - / - / 2.00E-02 / - / - / 2.51E-02
Transport_RAN regulation pathway / 2.51E-02 / - / - / - / 3.16E-02 / - / - / 3.16E-02
Development_POTCH-induced EMT / 2.51E-02 / - / - / - / 3.16E-02 / - / - / 3.16E-02
Cell cycle_Cell cycle (generic schema) / 2.51E-02 / - / - / - / 3.16E-02 / - / - / 3.98E-02
Immune response_IL-15 signaling via JAK-STAT cascade / 3.16E-02 / - / - / - / 3.98E-02 / - / - / 3.98E-02
Immune response_MIF-JAB1 signaling / 3.16E-02 / - / - / - / 3.98E-02 / - / - / 3.98E-02
Muscle contraction_nnos Signaling in Skeletal Muscle / 3.98E-02 / - / - / - / 3.98E-02 / - / - / 5.01E-02
Immune response_IL-6 signaling pathway / 3.98E-02 / - / - / - / 5.01E-02 / - / - / 5.01E-02
Cell cycle_ESR1 regulation of G1/S transition / 3.98E-02 / - / - / - / 5.01E-02 / - / - / 5.01E-02
Immune response_Alternative complement pathway / 5.01E-02 / 2.00E-02 / - / - / 6.31E-02 / - / 3.16E-02 / 6.31E-02
Apoptosis and survival_Apoptotic TNF-family pathways / 5.01E-02 / 2.00E-02 / - / - / 6.31E-02 / - / 3.98E-02 / 6.31E-02
Mucin expression in CF via IL-6, IL-17 signaling pathways / 5.01E-02 / - / - / 1.26E-02 / 5.01E-02 / 2.00E-02 / 3.16E-02 / 6.31E-02
Development_POTCH1-mediated pathway for NF-KB activity modulation / 5.01E-02 / - / - / - / 5.01E-02 / - / - / 6.31E-02
Development_Growth hormone signaling via stats and PLC/IP3 / 5.01E-02 / - / - / - / 5.01E-02 / - / - / 6.31E-02
DNA damage_Nucleotide excision repair / 5.01E-02 / - / - / - / 5.01E-02 / - / - / 6.31E-02
Development_MAG-dependent inhibition of neurite outgrowth / 5.01E-02 / - / - / - / 6.31E-02 / - / - / 6.31E-02
Development_Growth hormone signaling via PI3K/AKT and MAPK cascades / 5.01E-02 / - / - / - / 6.31E-02 / - / - / 6.31E-02
Immune response_Bacterial infections in normal airways / 6.31E-02 / - / - / 2.00E-02 / 7.94E-02 / 3.16E-02 / 3.98E-02 / 7.94E-02
Mucin expression in CF via tlrs, EGFR signaling pathways / 6.31E-02 / - / - / 2.00E-02 / 7.94E-02 / 3.16E-02 / 3.98E-02 / 7.94E-02
Immune response_TREM1 signaling pathway / 7.94E-02 / - / - / 2.00E-02 / 7.94E-02 / 3.16E-02 / 5.01E-02 / 1.00E-01
Immune response_TLR signaling pathways / 7.94E-02 / - / - / 2.00E-02 / 7.94E-02 / 3.16E-02 / 5.01E-02 / 1.00E-01
Bacterial infections in CF airways / 7.94E-02 / - / - / 2.00E-02 / 1.00E-01 / 3.16E-02 / 5.01E-02 / 1.00E-01
Transport_macropinocytosis / - / 6.31E-03 / - / - / 2.00E-02 / - / 1.00E-02 / -
Normal wtcftr traffic / Sorting endosome formation / - / 7.94E-03 / - / - / 3.16E-02 / - / 1.58E-02 / -
Cell cycle_Chromosome condensation in prometaphase / - / 1.00E-02 / - / - / 3.16E-02 / - / 2.00E-02 / -
Delta508-CFTR traffic / Sorting endosome formation in CF / - / 1.26E-02 / - / - / 3.98E-02 / - / 2.00E-02 / -
Transport_Clathrin-coated vesicle cycle / - / 3.16E-02 / - / - / 1.00E-01 / - / 6.31E-02 / -
Cytoskeleton remodeling_Alpha-1A adrenergic receptor-dependent inhibition of PI3K / - / - / 6.31E-03 / - / - / 1.26E-02 / - / 3.16E-02
Development_Alpha-1 adrenergic receptors signaling via camp / - / - / 6.31E-03 / - / - / 1.26E-02 / - / 3.16E-02
Cytoskeleton remodeling_Role of PKA in cytoskeleton reorganisation / - / - / 1.58E-02 / 1.58E-02 / - / 2.51E-02 / 3.16E-02 / 6.31E-02
Development_Activation of ERK by Alpha-1 adrenergic receptors / - / - / 1.58E-02 / - / - / 2.51E-02 / - / 7.94E-02
Glycolysis and gluconeogenesis p. 1 / - / - / 1.58E-02 / - / - / 2.51E-02 / - / 7.94E-02
Regulation of metabolism_Triiodothyronine and Thyroxine signaling / - / - / 1.58E-02 / - / - / 3.16E-02 / - / 7.94E-02
Translation_Translation regulation by Alpha-1 adrenergic receptors / - / - / 2.00E-02 / - / - / 3.16E-02 / - / 7.94E-02
Cardiac Hypertrophy_Ca(2+)-dependent NF-AT signaling in Cardiac Hypertrophy / - / - / 2.00E-02 / - / - / 3.16E-02 / - / 1.00E-01
Glycolysis and gluconeogenesis (short map) / - / - / 2.51E-02 / - / - / 3.98E-02 / - / 1.00E-01
Regulation of lipid metabolism_Alpha-1 adrenergic receptors signaling via arachidonic acid / - / - / 2.51E-02 / - / - / 3.98E-02 / - / -
Fructose metabolism / - / - / 2.51E-02 / - / - / 3.98E-02 / - / -
Fructose metabolism/ Rodent version / - / - / 3.16E-02 / - / - / 5.01E-02 / - / -
Muscle contraction_ gpcrs in the regulation of smooth muscle tone / - / - / 3.16E-02 / - / - / 5.01E-02 / - / -
Chemotaxis_CCR4-induced leukocyte adhesion / - / - / - / 1.00E-02 / - / 2.00E-02 / 2.51E-02 / -
Immune response_IL-5 signaling / - / - / - / 1.58E-02 / - / 2.51E-02 / 3.98E-02 / -
Chemotaxis_Inhibitory action of lipoxins on IL-8- and Leukotriene B4-induced neutrophil migration / - / - / - / 2.00E-02 / - / 3.16E-02 / 3.98E-02 / -
Cell adhesion_Integrin inside-out signaling / - / - / - / 2.00E-02 / - / 3.16E-02 / 5.01E-02 / -
Inhibitory action of Lipoxins on neutrophil migration / - / - / - / 2.00E-02 / - / 3.16E-02 / 5.01E-02 / -
Immune response _Immunological synapse formation / - / - / - / 2.00E-02 / - / 3.98E-02 / 5.01E-02 / -
Chemotaxis_Leukocyte chemotaxis / - / - / - / 2.51E-02 / - / 5.01E-02 / 6.31E-02 / -

*The numbers in the figure represent p values for the GeneGo pathway maps. All values are significant with p < 0.1; O-E = ossified early; O-L = ossified late;PO-E =poorly ossified early;PO-L =poorly ossified late; O = ossified total;PO =poorly ossified total, in which O signifies the ossified marrow explants, PO signifies the poorly ossified marrow explants, E (early) stands for the samples collected in Days 12-14, and L (late) stands for the samples collected in Days 157-28. O or PO, when used alone, signifies the samples collected for all days (12-28) for the ossified or poorly ossified groups. E or L, when used alone, signify the samples collected in Days 12-14 (early) or Days 157-28 (late) for both ossified and poorly ossified groups.