Supplemental Table 4. Genego Pathway Maps Obtained Using Ontology Enrichment, Proteins
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 / ENiacin-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.