Supplemental Digital Content 2 -Table 2
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Supplemental Digital Content 2 -Table 2- Complete list of pathways associated with the genes identified a differentially expressed between NA and IF/TA samples. Category ID Name Source P-value 1.33E- Pathway hsa05332 Graft-versus-host disease KEGG pathway 16 2.35E- Pathway hsa05330 Allograft rejection KEGG pathway 15 5.12E- Pathway hsa04650 Natural killer cell mediated cytotoxicity KEGG pathway 15 2.11E- Pathway hsa04940 Type I diabetes mellitus KEGG pathway 13 2.02E- Pathway hsa04612 Antigen processing and presentation KEGG pathway 12 1.74E- Pathway hsa04514 Cell adhesion molecules (CAMs) il12_2path Pathway way NCI-Nature IL12-mediated signaling events tcr_pathw Pathway ay KEGG pathway Curated NCI-Nature TCR signaling in naïve CD4+ T cells Curated 11 3.50E11 3.38E10 4.19E- Pathway hsa05320 Autoimmune thyroid disease KEGG pathway 10 6.25EPathway hsa05340 Primary immunodeficiency KEGG pathway h_tcraPath Lck and Fyn tyrosine kinases in Pathway way initiation of TCR Activation 10 1.06E- CGAP BioCarta 09 1.31E- Pathway P00053 T cell activation cd8tcrpath Pathway way PantherDB NCI-Nature TCR signaling in naïve CD8+ T cells Curated 09 2.77E09 6.39E- Pathway hsa04660 T cell receptor signaling pathway KEGG pathway TCRAPA Pathway THWAY 6.46ETCRAPATHWAY MSigDB h_tcytotox Pathway icPathway athway T Cytotoxic Cell Surface Molecules CGAP BioCarta pathway T Helper Cell Surface Molecules CGAP BioCarta NCI-Nature IL12 signaling mediated by STAT4 Curated Inflammation mediated by chemokine Pathway P00031 09 6.46E- il12_stat4 Pathway 09 6.46E- h_thelperP Pathway 09 and cytokine signaling 09 2.21E08 2.52E- PantherDB 08 TCYTOT OXICPAT Pathway HWAY 2.84ETCYTOTOXICPATHWAY MSigDB 08 Pathway h_ctlPath CTL mediated immune response against way target cells 2.84ECGAP BioCarta 08 THELPE RPATHW Pathway AY 2.84ETHELPERPATHWAY MSigDB CTLPAT Pathway HWAY 1.00ECTLPATHWAY MSigDB h_tcrPath Pathway way 08 07 2.10E- T Cell Receptor Signaling CGAP BioCarta 07 h_tcapopt osisPathw Pathway Pathway 2.14E- ay HIV Induced T Cell Apoptosis CGAP BioCarta fcer1path Fc-epsilon receptor I signaling in mast NCI-Nature way cells Curated 07 2.72E07 Activation of Csk by cAMP-dependent Pathway h_CSKPat Protein Kinase Inhibits Signaling hway through the T Cell Receptor 4.64ECGAP BioCarta 07 8.41E- Pathway hsa04640 Hematopoietic cell lineage KEGG pathway 07 CTLA4P ATHWA 1.02E- Pathway Y CTLA4PATHWAY MSigDB 06 Pathway TCAPOP TCAPOPTOSISPATHWAY MSigDB 1.11E- TOSISPA 06 THWAY ST_T_CE LL_SIGN AL_TRA NSDUCTI ST_T_CELL_SIGNAL_TRANSDUCTI Pathway ON ON 1.22EMSigDB APOPTO Pathway Pathway 1.84E- SIS APOPTOSIS h_ctla4Pat The Co-Stimulatory Signal During T- hway cell Activation cxcr4_pat Pathway hway 06 MSigDB 2.11ECGAP BioCarta NCI-Nature CXCR4-mediated signaling events 06 Curated 06 2.24E06 7.36E- Pathway hsa04662 B cell receptor signaling pathway KEGG pathway CSKPAT Pathway HWAY 7.81ECSKPATHWAY MSigDB AMIPAT Pathway HWAY HWAY 06 7.81E- AMIPATHWAY MSigDB TCRPAT Pathway 06 06 1.54E- TCRPATHWAY MSigDB 05 1.62E- Pathway hsa05310 Asthma KEGG pathway 05 Pathway h_IL12Pat IL12 and Stat4 Dependent Signaling in hway Th1 Development 1.80ECGAP BioCarta 05 NO2IL12 PATHWA Pathway Y 1.87ENO2IL12PATHWAY bcr_5path Pathway Pathway MSigDB NCI-Nature way BCR signaling pathway h_nktPath Selective expression of chemokine way receptors during T-cell polarization Curated HWAY 2.37E05 2.47E- CGAP BioCarta IL12PAT Pathway 05 05 6.13E- IL12PATHWAY MSigDB 05 1.22E- Pathway hsa04620 Toll-like receptor signaling pathway KEGG pathway 04 1.23E- Pathway hsa04060 Cytokine-cytokine receptor interaction KEGG pathway nstreampa Downstream signaling in naïve CD8+ T NCI-Nature thway cells Curated 04 cd8tcrdow Pathway il23pathw Pathway ay NCI-Nature IL23-mediated signaling events Curated D4GDIPA 1.80E04 3.16E04 3.39E- Pathway THWAY D4GDIPATHWAY MSigDB Pathway P00006 Apoptosis signaling PantherDB 04 3.66E- 04 APOPTO SIS_GEN Pathway MAPP 4.48EAPOPTOSISP MSigDB NKTPAT Pathway HWAY 04 1.09E- NKTPATHWAY MSigDB 03 TH1TH2P ATHWA Pathway Y 1.16ETH1TH2PATHWAY MSigDB h_tcrmole Pathway cule 03 1.31E- T Cell Receptor and CD3 Complex CGAP BioCarta 03 BLYMPH OCYTEP ATHWA Pathway Y 1.43EBLYMPHOCYTEPATHWAY PW:00002 Pathway 34 innate immune response MSigDB 03 Pathway 1.43E- Ontology 03 h_blymph ocytePath Pathway way 1.43EB Lymphocyte Cell Surface Molecules CGAP BioCarta 03 MONOC YTEPAT Pathway HWAY 1.43EMONOCYTEPATHWAY MSigDB 03 h_monocy Pathway tePathway 1.43EMonocyte and its Surface Molecules CGAP BioCarta 03 h_granulo Pathway cytesPath Adhesion and Diapedesis of way Granulocytes 1.51ECGAP BioCarta h_d4gdiPa Pathway thway 03 1.51E- D4-GDI Signaling CGAP BioCarta 03 APOPTO SIS_KEG Pathway G 1.94EAPOPTOSISG MSigDB h_th1th2P Pathway athway 03 1.99E- Th1/Th2 Differentiation CGAP BioCarta 03 NKCELL SPATHW Pathway AY 1.99ENKCELLSPATHWAY MSigDB 03 h_neutrop hilPathwa Pathway y 2.12ENeutrophil and Its Surface Molecules CGAP BioCarta h_bbcellP Pathway athway 03 2.12E- Bystander B Cell Activation CGAP BioCarta 03 BBCELL PATHWA Pathway Y 2.12EBBCELLPATHWAY MSigDB 03 NEUTRO PHILPAT Pathway HWAY 2.12ENEUTROPHILPATHWAY MSigDB h_il17Path Pathway way 2.84EIL 17 Signaling il6_7path Pathway way CGAP BioCarta NCI-Nature IL6-mediated signaling events Curated IL17PAT Pathway HWAY way 03 3.99E03 5.06E- IL17PATHWAY pi3kcipath Pathway 03 MSigDB NCI-Nature Class I PI3K signaling events Curated 03 5.43E03 LYMPHO CYTEPA Pathway THWAY 6.01ELYMPHOCYTEPATHWAY MSigDB 03 h_lympho cytePathw Pathway ay 6.01EAdhesion Molecules on Lymphocyte CGAP BioCarta 03 CALCINE URIN_NF _AT_SIG Pathway NALING 6.05ECALCINEURIN_NF_AT_SIGNALING MSigDB TCRMOL Pathway ECULE 03 7.45E- TCRMOLECULE MSigDB 03 CASPAS EPATHW Pathway AY 8.10ECASPASEPATHWAY MSigDB 03 8.14E- Pathway P00010 B cell activation PantherDB h_tnfr2Pat Pathway hway 8.60ETNFR2 Signaling CGAP BioCarta TNFR2PA Pathway THWAY 03 03 8.60E- TNFR2PATHWAY MSigDB 03 8.95E- Pathway 163200 Electron Transport Chain Reactome Valine, leucine and isoleucine Pathway hsa00280 degradation 30 2.21E- KEGG pathway 26 1.16E- Pathway hsa00190 Oxidative phosphorylation KEGG pathway 25 2.52E- Pathway hsa05012 Parkinson's disease KEGG pathway 21 OXIDATI VE_PHO SPHORY Pathway Pathway 1.59E- LATION OXIDATIVE_PHOSPHORYLATION VALINE_ VALINE_LEUCINE_AND_ISOLEUCI LEUCINE NE_DEGRADATION MSigDB 17 1.98E- MSigDB 17 _AND_IS OLEUCI NE_DEG RADATI ON 2.84EPathway hsa05010 Alzheimer's disease KEGG pathway 17 2.89E- Pathway 71291 Metabolism of nitrogenous molecules Reactome 17 8.95E- Pathway hsa05016 Huntington's disease KEGG pathway 17 MAP0028 0_Valine_ leucine_an d_isoleuci Pathway ne_degrad MAP00280 Valine leucine and ation isoleucine degradation PW:00000 Pathway 34 3.31EGenMAPP Pathway oxidative phosphorylation Ontology 16 8.37E16 1.92E- Pathway hsa00071 Fatty acid metabolism KEGG pathway 15 7.62E- Pathway PWY-561 glyoxylate cycle II BioCyc 15 AERESP Pathway DON- aerobic respiration -- electron donors PWY reaction list 3.08EBioCyc 14 5.46E- Pathway hsa00640 Propanoate metabolism KEGG pathway 14 6.88E- Pathway hsa00650 Butanoate metabolism KEGG pathway 14 5.32E- Pathway hsa00020 Citrate cycle (TCA cycle) KEGG pathway 13 PROPAN OATE_M ETABOLI Pathway SM 5.32EPROPANOATE_METABOLISM MSigDB 13 KREBS_T CA_CYC Pathway LE 2.39EKREBS_TCACLE MSigDB Oxidative decarboxylation of pyruvate Pathway 71406 and TCA cycle 11 7.35E- Reactome 11 CITRATE _CYCLE_ TCA_CY 5.96E- Pathway CLE CITRATECLE_TCACLE MSigDB Pathway MAP0064 MAP00640 Propanoate metabolism GenMAPP 09 2.39E- 0_Propano 08 ate_metab olism PW:00000 Pathway 26 Pathway citrate cycle Ontology 2.39E08 MAP0007 1_Fatty_a cid_metab Pathway Pathway olism 2.53EMAP00071 Fatty acid metabolism GenMAPP PW:00000 valine, leucine and isoleucine Pathway 71 Ontology degradation 08 3.35E08 BUTANO ATE_ME TABOLIS Pathway M 6.40EBUTANOATE_METABOLISM MSigDB 08 MAP0019 0_Oxidati ve_phosph Pathway orylation 1.05EMAP00190 Oxidative phosphorylation PW:00000 Pathway 43 GenMAPP Pathway pyruvate metabolic Ontology UBIQUIN Pathway ONE_BIO UBIQUINONE_BIOSYNTHESIS 07 1.20E07 1.22E- MSigDB 07 SYNTHE SIS MAP0062 0_Pyruvat e_metabol Pathway ism 2.19EMAP00620 Pyruvate metabolism GenMAPP 07 MAP0065 0_Butanoa te_metabo Pathway lism 2.42EMAP00650 Butanoate metabolism GenMAPP FAOPathway PWY 07 2.56E- fatty acid oxidation I BioCyc 07 2.75E- Pathway hsa00620 Pyruvate metabolism KEGG pathway 07 3.67E- Pathway TCA TCA cycle -- aerobic respiration BioCyc 07 TCA/GLY Pathway OX- superpathway of glyoxylate BYPASS bypass+TCA PW:00000 Pathway 64 3.67EBioCyc Pathway propanoate metabolic Ontology 07 4.20E07 6.75E- Pathway hsa00380 Tryptophan metabolism KEGG pathway 07 PYRUVA TE_MET ABOLIS Pathway M 1.14EPYRUVATE_METABOLISM PW:00000 Pathway 73 lysine degradation MSigDB 06 Pathway 3.54E- Ontology 06 REDUCTI VE_CAR BOXYLA TE_CYC LE_CO2_ Pathway FIXATIO REDUCTIVE_CARBOXYLATECLE_ N CO2_FIXATION 3.54EMSigDB 06 5.07E- Pathway hsa00410 beta-Alanine metabolism KEGG pathway 06 GLYCOL YSIS_AN D_GLUC ONEOGE Pathway NESIS 6.26ES_AND_GLUCONEOGENESIS MSigDB 06 MAP0031 0_Lysine_ Pathway degradatio 9.80EMAP00310 Lysine degradation GenMAPP 06 n P105Pathway PWY 1.11ETCA cycle variation VIII BioCyc 05 ARGININ E_AND_P ROLINE_ Pathway METABO ARGININE_AND_PROLINE_METAB LISM OLISM PW:00000 Pathway 50 arginine and proline metabolic 1.94EMSigDB 05 Pathway 2.19E- Ontology 05 MAP0002 0_Citrate_ cycle_TC Pathway A_cycle 4.75EMAP00020 Citrate cycle TCA cycle GenMAPP 05 BETA_A LANINE_ METABO Pathway LISM 5.11EBETA_ALANINE_METABOLISM PW:00000 Pathway 58 fatty acid metabolic MSigDB 05 Pathway 7.42E- Ontology Urea cycle and metabolism of amino 05 8.41E- Pathway hsa00220 groups KEGG pathway Pathway GLYCOL superpathway of glycolysis, pyruvate BioCyc 05 1.21E- YSIS/TC dehydrogenase, TCA, and glyoxylate A/GLYO bypass 04 XBYPASS MAP0038 0_Tryptop han_meta Pathway bolism 1.48EMAP00380 Tryptophan metabolism GenMAPP ILEUDEG Pathway -PWY 04 3.99E- isoleucine degradation I BioCyc 04 TRYPTO PHAN_M ETABOLI Pathway SM 4.40ETRYPTOPHAN_METABOLISM MSigDB 04 MAP0033 0_Arginin e_and_pro Pathway line_meta MAP00330 Arginine and proline bolism metabolism 5.53EGenMAPP superpathway of glycolysis and TCA Pathway PWY1G-2 variant VIII 04 5.53E- BioCyc 04 6.01E- Pathway hsa00010 Glycolysis / Gluconeogenesis KEGG pathway 04 MAP0063 0_Glyoxyl ate_and_d icarboxyla Pathway te_metabo MAP00630 Glyoxylate and lism dicarboxylate metabolism 6.45EGenMAPP 04 MAP0072 0_Reducti ve_carbox ylate_cycl Pathway e_CO2_fi MAP00720 Reductive carboxylate cycle xation CO2 fixation 6.49EGenMAPP 04 MAP0006 2_Fatty_a cid_biosy Pathway nthesis_pa MAP00062 Fatty acid biosynthesis path th_2 2 PW:00000 Pathway 77 54 GenMAPP Pathway beta-alanine metabolic PW:00000 Pathway 6.49E- Ontology Pathway tryptophan metabolic Ontology GLYCOL Pathway YSIS 04 8.78E04 9.17E04 1.17E- GLYCOLYSIS MSigDB 03 GLUCON EOGENE Pathway SIS 1.17EGLUCONEOGENESIS MSigDB 03 1.50E- Pathway P00051 TCA cycle PantherDB 03 ILEUDEG2Pathway PWY 1.67Eisoleucine degradation III BioCyc 03 PHENYL ALANIN E-DEG1Pathway PWY 1.67Ephenylalanine degradation I PW:00000 Pathway 65 BioCyc Pathway butanoate metabolic Ontology 03 1.77E03 1.77E- Pathway P04372 5-Hydroxytryptamine degredation PantherDB 03 2.53E- Pathway 73923 Lipid metabolism PW:00000 Pathway 52 Reactome Pathway tyrosine metabolic Ontology 03 3.34E03 GLYOXY Pathway LATE_A GLYOXYLATE_AND_DICARBOXY ND_DIC LATE_METABOLISM 3.79EMSigDB 03 ARBOXY LATE_M ETABOLI SM MAP0025 2_Alanine _and_aspa Pathway rtate_meta MAP00252 Alanine and aspartate bolism metabolism 3.88EGenMAPP 03 4.04E- Pathway hsa00310 Lysine degradation KEGG pathway 03 LYSINE_ DEGRAD Pathway ATION 4.10ELYSINE_DEGRADATION MSigDB 03 MAP0001 0_Glycoly sis_Gluco neogenesi Pathway s 5.20EMAP00010 Glycolysis Gluconeogenesis GenMAPP 03 MITOCH ONDRIA L_FATTY MITOCHONDRIAL_FATTY_ACID_B Pathway _ACID_B ETAOXIDATION 5.95EMSigDB 03 ETAOXI DATION MAP0041 0_beta_Al anine_met Pathway abolism 5.95EMAP00410 beta Alanine metabolism GenMAPP 03 ALANIN E_AND_ ASPART ATE_ME Pathway TABOLIS ALANINE_AND_ASPARTATE_MET M ABOLISM 6.19EMSigDB 03 FATTY_ ACID_BI OSYNTH Pathway ESIS_PA FATTY_ACID_BIOSYNTHESIS_PAT TH_2 H_2 6.95EMSigDB Synthesis and degradation of ketone Pathway hsa00072 bodies 6.95EKEGG pathway VALDEG Pathway -PWY athway 03 7.74E- valine degradation I BioCyc h_malateP Pathway 03 03 8.53E- Malate-aspartate shuttle CGAP BioCarta 03 PYRUVD EHYDPathway PWY 8.53Epyruvate dehydrogenase BioCyc 03 ADENOS YLHOM OCYSCA Pathway T-PWY 8.53Emethionine biosynthesis IV BioCyc GLUTOX Pathway A-PWY 03 8.53E- glutamate degradation VII BioCyc 03
