EN Supplemental Figure 1: IVF experimental strategy. Supplemental Figure 2:

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1 EN Supplemental Figure 1: IVF experimental strategy. Cumulous-oocyte-complexes were isolated from superovulated C57Bl/6J females and incubated with previously capacitated caudal epididymal sperm. Following fertilization, zygotes were washed and cultured either under suboptimal WM and 20% oxygen conditions (IVF WM, red), or superior KAA medium with 5% oxygen conditions (IVF KAA, yellow). Blastocysts were used for molecular experiments or transferred into pseudo pregnant CF1 recipients, and newborn mice were maintained into adulthood for subsequent physiological and molecular analyses. As a control, C57Bl/6J females were superovulated and mated overnight with C57Bl/6J males. In vivogenerated blastocysts were isolated 96hrs post-fertilization, used directly in experiments, or transferred to recipients (flushed blastocyst/fb group, blue). Supplemental Figure 2: Conception by IVF WM reduces growth and impairs glucose tolerance. (A) Postnatal growth curves depicting average body weight for male FB (blue) and IVF WM (red) mice. (B) Male intraperitoneal glucose tolerance test (IPGTT) sampled at 19wks for clearance of a 1.5mg/g glucose bolus over 120 min, with area under the curve (AUC) calculated from total glucose levels measured during the entire IPGTT course. (C) Postnatal growth of female FB and IVF WM animals, and (D) female IPGTT sampled in tandem with males. For all measurements, FB males n=8, IVF WM males n=12, FB females n=6, IVF WM females n=8. Error bars depict standard error of the mean, *p<0.05. IVF WM mice display altered metabolic and physiological parameters at 40wks of age. (A) Serum insulin, leptin and corticosterone in male FB and IVF WM animals with (B) parallel measurements in females. At sacrifice, selected morphological measurements included (C) body weight, (D) body mass index (BMI), and (E) anogenital distance. (F,G) Organ weights were normalized as percent body weight for (F) male and (G) female FB and IVF WM males and females. Individual sample sizes are shown in (A,B); sample size for (C-G) was: FB males n=8, IVF WM males n=12, FB females n=5, IVF WM females n=8. Error bars depict standard error of the mean, *p<0.05. Supplemental Figure 3: Histological analysis of glomeruli and pancreatic islets. Histological analysis of (A) FB and (B) IVF WM male kidneys at 40wks revealed no significant changes in (C) number of glomeruli (open arrowheads) or (D) glomerular volume. Analysis conducted on n-5 mice per condition. Immunostaining of insulin in (E) FB and (F) IVF WM male pancreata at 40wks showed no changes in (G) percent of insulin positive tissue. Analysis conducted on n=4 mice per condition. Scale bars represent 300mm, error bars depict standard deviation. Supplemental Figure 4: Intraperitoneal glucose tolerance test performed on female FB (blue) and IVF KAA (yellow) animals aged (A) 13wks, (B) 20wks, and (C) 29wks, with area under the curve (AUC) measured from total glucose levels during entire IPGTT course. For all time points, FB n=8 and IVF KAA n=7 females. Error bars depict standard deviation, *p<0.05. Supplemental Figure 5: IVF KAA morphometric parameters at sacrifice. Comparison of morphological parameters between FB (blue) and IVF KAA (yellow) animals at sacrifice (30wks), including (A) weight, (B) body mass index (BMI), (C) crown-rump length, (D) anogenital distance, (E) anogenital index, or (F) biparietal diameter (BPD). (G-H) Organ sizes depicted as relative body weights for (G) male and (H) female FB and IVF KAA animals. For all measurements, sample size was: FB males n=8, IVF KAA males n=8-14, FB females n=5-8, IVF KAA females n=5-8. Error bars depict standard deviation, *p<0.05.

2 Supplemental Figure 6: Normal in IVF KAA males. (A) Postnatal growth of FB (blue) and IVF KAA (yellow) males, showing periodic intraperitoneal glucose tolerance sampling (IPGTT) and the administration of a high fat diet beginning at 24wks. (B-D) IPGTT of glucose handling at (B) 13wks, (C) 20wks, and (D) 29wks of age, with corresponding area under the curve (AUC) measured form total glucose levels during entire IPGTT course. (E) Average daily food intake monitored over five-day period. (F) Serum insulin measured at 11wks. (G-I) Intermittent DEXA scanning of (G) bone mineral density and (H) fat content, with calculated (I) percent fat gain in FB and IVF KAA males. Sample size indicated on graphs; DEXA sample size was FB males n=8 and IVF KAA males n=14. Error bars depict standard deviation, *p<0.05. Supplemental Figure 7: DNA methylation analysis of the Txnip locus. Bisulfite sequencing of DNA methylation profiles at the Txnip promoter and 5 UTR revealed no changes in CpG methylation between FB (n=3) and IVF KAA (n=3) blastocysts.

3 Supplemental Figure 1 C57Bl/6J X C57Bl/6J Preimplantation development IVFWM / IVFKAA Embryo culture Culture medium KAA or WM Oxygen tension 5% or 20% Blastocyst transfer In vivo Blastocysts flushed from the uterine horns Molecular experiments Placentation & fetal growth CF1 Postnatal development IVFWM / IVFKAA experimental group Newborn/adult mice Physiological observations Molecular experiments Flushed blastocyst (FB) control group

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5 Supplemental Figure 3 A B C FB D IVFWM E F G FB IVFWM

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9 Supplemental Figure 7 CpG sites: TATA-box ATG Exon TSS IVFKAA FB methylated unmethylated

10 Supplemental Table 1A Males Females Physiological parameter FB (n=8) IVF WM (n=20) FB (n=7) IVF WM (n=13) Birth weight (g) 1.73 ± ± ± ± 0.05 AGD (mm) 1.85 ± ± ± ± 0.06 AGI (mm/g) 1.07 ± * ± ± ± 0.04 Head diameter (mm) 7.63 ± ± ± ± 0.12 Abdominal diameter (mm) 9.68 ± ± ± ± 0.17 Crown-rump length (mm) ± ± ± ± 0.52 BMI (g/cm 2 ) ± ± ± ± Supplemental Table 1B FB (n=14) IVF KAA (n=11) Litter size (# pups) 9.50 ± * ± 0.58 Survival (%) 58.9 ± * ± 2.8 Sex (% males) 54.5 ± ± 8.8 Males Females Physiological parameter FB (n=9) IVF KAA (n=15) FB (n=8) IVF KAA (n=10) Birth weight (g) 1.51 ± ± ± * ± 0.06 AGD (mm) 1.84 ± ± ± * ± 0.05 AGI (mm/g) 1.23 ± ± ± ± 0.06 Head diameter (mm) 7.64 ± ± ± * ± 0.14 Abdominal diameter (mm) 9.92 ± ± ± ± 0.44 Crown-rump length (mm) ± ± ± * ± 0.48 BMI (g/cm 2 ) ± ± ± ± Morphometric parameters measured in FB WM, IVF WM, FB KAA and IVF KAA pups at birth. AGD, anogenital distance; AGI, anogenital index; BMI, body mass index. Values are ±SEM, with p<0.05 indicated by * in bold.

11 Supplemental Table 2. Comprehensive list of metabolites detected by non-targeted mass spectrometry (Metabolon, Inc.) in FB and IVFKAA female serum at 29wks. The Fold IVF KAA Individual IVF values normalized to FB mean Pathway Subpathay Biochemical Platform Change FB p-value IVFKAA 1 IVFKAA 2 IVFKAA 3 IVFKAA 4 Amino acid Glycine, serine glycine GC/MS and threonine dimethylglycine GC/MS N-acetylglycine GC/MS beta-hydroxypyruvate GC/MS serine GC/MS threonine LC/MS pos betaine LC/MS pos Alanine and aspartate GC/MS aspartate asparagine GC/MS ureidopropionate LC/MS pos N-acetyl-beta-alanine LC/MS pos alanine GC/MS N-acetylalanine LC/MS neg N-acetylaspartate (NAA) GC/MS Glutamate glutamate GC/MS glutamine LC/MS pos N-acetylglutamate LC/MS pos Histidine histidine LC/MS neg trans-urocanate LC/MS pos Lysine lysine LC/MS pos aminoadipate LC/MS pos pipecolate LC/MS pos glutaroyl carnitine LC/MS pos Phenylalanine & phenylalanine LC/MS pos tyrosine phenylacetate LC/MS neg p-cresol sulfate LC/MS neg tyrosine LC/MS pos (4-hydroxyphenyl)lactate LC/MS neg Tryptophan 4-hydroxyphenylpyruvate LC/MS neg N-acetylphenylalanine LC/MS pos N-acetyltyrosine LC/MS neg phenylacetylglycine LC/MS neg phenol sulfate LC/MS neg p-toluic acid GC/MS kynurenate LC/MS neg kynurenine LC/MS pos tryptophan LC/MS pos indolelactate GC/MS indolepyruvate LC/MS neg serotonin (5HT) LC/MS pos N-acetyltryptophan LC/MS neg C-glycosyltryptophan* LC/MS pos

12 Valine, leucine and isoleucine 3-indoxyl sulfate LC/MS neg indolepropionate LC/MS neg methyl-2-oxobutyrate LC/MS neg methyl-2-oxovalerate LC/MS neg beta-hydroxyisovalerate LC/MS neg alpha-hydroxyisocaproate LC/MS neg isoleucine LC/MS pos leucine LC/MS pos N-acetylleucine LC/MS pos N-acetylisoleucine LC/MS pos valine LC/MS pos hydroxyisobutyrate GC/MS methyl-2-oxopentanoate LC/MS neg alpha-hydroxyisovalerate LC/MS neg isovalerylglycine LC/MS pos isobutyrylcarnitine LC/MS pos hydroxy-3-methylvalerate LC/MS neg methylbutyroylcarnitine LC/MS pos isovalerylcarnitine LC/MS pos hydroxyisovaleroyl carnitine LC/MS pos methylglutaroylcarnitine LC/MS pos isobutyrylglycine LC/MS pos Cysteine, cysteine GC/MS methionine, SAM, N-formylmethionine LC/MS neg taurine taurine GC/MS methionine LC/MS pos N-acetylmethionine LC/MS neg hydroxybutyrate (AHB) GC/MS Urea cycle; arginine-, proline-, Creatine Butanoate Polyamine dimethylarginine (SDMA + LC/MS pos ADMA) arginine LC/MS pos ornithine GC/MS urea GC/MS proline LC/MS pos citrulline LC/MS pos trans-4-hydroxyproline GC/MS homocitrulline LC/MS pos creatine LC/MS pos creatinine LC/MS pos aminobutyrate GC/MS methylthioadenosine (MTA) LC/MS pos

13 Glutathione S-methylglutathione LC/MS pos oxoproline LC/MS neg glutathione, oxidized (GSSG) LC/MS pos cysteine-glutathione disulfide LC/MS pos Peptide ophthalmate LC/MS pos Dipeptide alanylalanine GC/MS gamma-glutamyl gamma-glutamylvaline LC/MS pos gamma-glutamylleucine LC/MS pos gamma-glutamylisoleucine* LC/MS pos Fibrinogen cleavage peptide Carbohydrate Aminosugars Fructose, mannose, galactose, starch, and Glycolysis, sucrose gluconeogenesis, pyruvate Energy Nucleotide sugars, pentose Krebs cycle Oxidative phosphorylation gamma-glutamylmethionine LC/MS pos gammaglutamylphenylalanine LC/MS pos gamma-glutamyltyrosine LC/MS pos gamma-glutamyltryptophan LC/MS pos gamma-glutamylalanine LC/MS pos TDTEDKGEFLSEGGGV* LC/MS pos TDTEDKGEFLSEGGGVR* LC/MS neg erythronate* GC/MS fructose GC/MS mannose GC/MS sorbitol GC/MS ,5-anhydroglucitol (1,5-AG) GC/MS glycerate GC/MS glucose GC/MS pyruvate GC/MS lactate GC/MS glucuronate GC/MS ribose GC/MS ribulose GC/MS arabinose GC/MS xylonate GC/MS citrate GC/MS cis-aconitate LC/MS neg alpha-ketoglutarate GC/MS succinate GC/MS succinylcarnitine LC/MS pos fumarate GC/MS malate GC/MS acetylphosphate GC/MS phosphate GC/MS

14 Lipid pyrophosphate (PPi) GC/MS Essential fatty acid linoleate (18:2n6) LC/MS neg linolenate [alpha or gamma; LC/MS neg (18:3n3 or 6)] dihomo-linolenate (20:3n3 or LC/MS neg n6) eicosapentaenoate (EPA; 20:5n3) LC/MS neg docosapentaenoate (n3 DPA; LC/MS neg :5n3) docosapentaenoate (n6 DPA; LC/MS neg :5n6) docosahexaenoate (DHA; 22:6n3) LC/MS neg Medium chain fatty acid Long chain fatty acid caproate (6:0) LC/MS neg heptanoate (7:0) LC/MS neg caprylate (8:0) LC/MS neg pelargonate (9:0) LC/MS neg caprate (10:0) LC/MS neg undecanoate (11:0) LC/MS neg undecenoate (11:1n1) LC/MS neg laurate (12:0) LC/MS neg myristate (14:0) LC/MS neg myristoleate (14:1n5) LC/MS neg palmitate (16:0) LC/MS neg palmitoleate (16:1n7) LC/MS neg margarate (17:0) LC/MS neg heptadecenoate (17:1n7) LC/MS neg stearate (18:0) LC/MS neg oleate (18:1n9) GC/MS cis-vaccenate (18:1n7) GC/MS stearidonate (18:4n3) LC/MS neg nonadecanoate (19:0) LC/MS neg nonadecenoate (19:1n9) LC/MS neg eicosenoate (20:1n9 or 11) LC/MS neg dihomo-linoleate (20:2n6) LC/MS neg mead acid (20:3n9) LC/MS neg arachidonate (20:4n6) LC/MS neg docosadienoate (22:2n6) LC/MS neg adrenate (22:4n6) LC/MS neg Fatty acid, methyl palmitate, methyl ester GC/MS ester Fatty acid, ester n-butyl Oleate GC/MS Fatty acid, 4-hydroxybutyrate (GHB) GC/MS monohydroxy

15 monohydroxy 16-hydroxypalmitate LC/MS neg hydroxystearate LC/MS neg hydroxypalmitate LC/MS neg HODE + 9-HODE LC/MS neg Fatty acid, 2-hydroxyglutarate GC/MS dicarboxylate sebacate (decanedioate) LC/MS neg hexadecanedioate LC/MS neg octadecanedioate LC/MS neg hydroxyadipate GC/MS Fatty acid, amide stearamide GC/MS Fatty acid, branched 15-methylpalmitate (isobar LC/MS neg with 2-methylpalmitate) 17-methylstearate LC/MS neg Eicosanoid 12-HETE LC/MS neg Fatty acid propionylcarnitine LC/MS pos (also butyrylcarnitine LC/MS pos BCAA Fatty acid ) valerylcarnitine LC/MS pos valerylglycine LC/MS pos isovalerate LC/MS neg hexanoylglycine LC/MS pos Carnitine deoxycarnitine LC/MS pos carnitine LC/MS pos dehydrocarnitine* LC/MS pos acetylcarnitine LC/MS pos hexanoylcarnitine LC/MS pos octanoylcarnitine LC/MS pos palmitoylcarnitine LC/MS pos stearoylcarnitine LC/MS pos oleoylcarnitine LC/MS pos Bile acid cholate LC/MS neg dehydrocholate LC/MS neg taurocholate LC/MS neg taurochenodeoxycholate LC/MS neg deoxycholate LC/MS neg taurodeoxycholate LC/MS neg beta-muricholate LC/MS neg alpha-muricholate LC/MS neg tauroursodeoxycholate LC/MS neg Glycerolipid glycerol GC/MS glycerol 3-phosphate (G3P) GC/MS Inositol glycerophosphorylcholine LC/MS pos (GPC) myo-inositol GC/MS inositol phosphate (I1P) GC/MS

16 Ketone bodies 3-hydroxybutyrate (BHBA) GC/MS Lysolipid palmitoylglycerophosphoetha nolamine 2- palmitoylglycerophosphoetha nolamine* LC/MS neg LC/MS neg LC/MS neg stearoylglycerophosphoethan olamine oleoylglycerophosphoethanol amine 2- oleoylglycerophosphoethanol amine* LC/MS neg LC/MS neg LC/MS neg linoleoylglycerophosphoethan olamine* 2- LC/MS neg linoleoylglycerophosphoethan olamine* arachidonoylglycerophospho ethanolamine* 2- arachidonoylglycerophospho ethanolamine* LC/MS neg LC/MS neg LC/MS pos docosahexaenoylglycerophos phoethanolamine* LC/MS pos myristoylglycerophosphocholi ne LC/MS pos palmitoylglycerophosphocholi ne 2- LC/MS pos 0.56 < palmitoylglycerophosphocholi ne* palmitoleoylglycerophosphoc holine* LC/MS pos

17 2- palmitoleoylglycerophosphoc holine* heptadecanoylglycerophosph ocholine LC/MS pos LC/MS pos LC/MS pos stearoylglycerophosphocholin e 2- LC/MS pos stearoylglycerophosphocholin e* oleoylglycerophosphocholine 2- oleoylglycerophosphocholine * linoleoylglycerophosphocholi ne 2- linoleoylglycerophosphocholi ne* arachidoylglycerophosphoch oline LC/MS pos 0.35 < LC/MS pos LC/MS pos LC/MS pos LC/MS pos LC/MS pos eicosadienoylglycerophospho choline* LC/MS pos 0.34 < eicosatrienoylglycerophospho choline* arachidonoylglycerophospho choline* 2- arachidonoylglycerophospho choline* docosapentaenoylglyceropho sphocholine* LC/MS pos LC/MS pos LC/MS pos LC/MS pos docosahexaenoylglycerophos phocholine*

18 Nucleotide Monoacylglycerol Sphingolipid Sterol/Steroid Purine, (hypo)xanthine/ino Purine, adenine containing Purine, guanine containing 2- LC/MS pos docosahexaenoylglycerophos phocholine* stearoylglycerophosphoinosit ol linoleoylglycerophosphoinosit ol* arachidonoylglycerophosphoi nositol* 2- arachidonoylglycerophosphoi nositol* LC/MS neg LC/MS neg LC/MS neg LC/MS neg LC/MS neg palmitoylplasmenylethanolam ine* palmitoylglycerol ( GC/MS monopalmitin) stearoylglycerol ( GC/MS monostearin) oleoylglycerol ( LC/MS pos monoolein) linoleoylglycerol ( LC/MS neg monolinolein) sphinganine LC/MS pos palmitoyl sphingomyelin GC/MS stearoyl sphingomyelin GC/MS cholesterol GC/MS dihydrocholesterol GC/MS corticosterone LC/MS pos alpha-hydroxy-3-oxo-4- cholestenoate (7-Hoca) LC/MS neg xanthine GC/MS xanthosine LC/MS pos adenosine LC/MS pos Nmethyladenosine LC/MS pos Nmethylguanosine LC/MS pos N6- carbamoylthreonyladenosine LC/MS pos Purine, urate Pyrimidine, cytidine containing urate LC/MS neg allantoin GC/MS cytidine LC/MS pos '-deoxycytidine LC/MS pos

19 Cofactors and vitamins Xenobiotics Pyrimidine, orotate Pyrimidine containing, thymine Pyrimidine containing, uracil containing Purine and pyrimidine Ascorbate and aldarate Hemoglobin and porphyrin Nicotinate and nicotinamide Pantothenate and CoA Pyridoxal Riboflavin Tocopherol Vitamin B6 Benzoate orotate GC/MS thymidine LC/MS neg uracil GC/MS ,6-dihydrouracil GC/MS uridine LC/MS neg pseudouridine LC/MS neg '-deoxyuridine LC/MS neg methylphosphate GC/MS gulono-1,4-lactone GC/MS ascorbate (Vitamin C) GC/MS threonate GC/MS glucurono-6,3-lactone LC/MS neg heme* LC/MS pos L-urobilin LC/MS pos bilirubin (E,E)* LC/MS pos biliverdin LC/MS pos nicotinamide GC/MS pantothenate LC/MS pos pyridoxal LC/MS pos flavin adenine dinucleotide LC/MS neg (FAD) riboflavin (Vitamin B2) LC/MS pos alpha-tocopherol GC/MS pyridoxate LC/MS neg hippurate LC/MS neg catechol sulfate LC/MS neg benzoate GC/MS hydroxybenzoate GC/MS methyl-4-hydroxybenzoate GC/MS Chemical Food component/plant Sugar, sugar substitute, starch glycolate (hydroxyacetate) GC/MS glycerol 2-phosphate GC/MS trizma acetate GC/MS ethylhexanoate GC/MS tartarate GC/MS ergothioneine LC/MS pos erythritol GC/MS

20 Supplemental Table 3. Evidence of metabolic perturbation in IVFKAA female liver, muscle, gonadal fat, and pancreatic islets at 29wks of age. The table shows canonical pathways significantly altered in IVFKAA tissues relative to FB controls as determined by Ingenuity Pathway Analysis (p<0.05, Fisher s exact test). Pathway p-value # Genes Gonadal Fat LXR/RXR Activation ALB,MLXIPL,APOB,MSR1,APOH,APOC3,APOF,SERPINA1,FGA,GC Atherosclerosis Signaling ALB,APOB,MSR1,SELP,APOC3,APOF,PLA2G5,SERPINA1,PDGFB Ephrin Receptor Signaling ROCK2,EPHB4,AKT2,SDCBP,GNA11,GNB5,ABL1,GNB1L,RASA1,PDGFB,GNG7 Nicotine Degradation III CYP2D6,CYP1A2,CYP4B1,AOX1,CYP2C18 Estrogen Biosynthesis CYP2D6,CYP1A2,CYP4B1,CYP2C18,AKR1C4 Bupropion Degradation CYP2D6,CYP1A2,CYP4B1,CYP2C18 Acetone Degradation I (to Methylglyoxal) CYP2D6,CYP1A2,CYP4B1,CYP2C18 Nicotine Degradation II CYP2D6,CYP1A2,CYP4B1,AOX1,CYP2C18 RhoGDI Signaling ROCK2,CDH5,GNA11,GNB5,CD44,MYL4,ARHGEF1,ARHGDIA,GNB1L,GNG7 Tyrosine Degradation I HPD,FAH Superpathway of Methionine Degradation BHMT,SUV39H2,MAT1A,PCCB Ephrin B Signaling ROCK2,EPHB4,GNA11,GNB5,GNB1L,GNG7 G Protein Signaling Mediated by Tubby GNB5,ABL1,GNB1L,GNG7 Extrinsic Prothrombin Activation Pathway FGB,FGA,FGG TREM1 Signaling AKT2,TYROBP,CASP1,LAT2,CD83 Coagulation System SERPINA1,FGB,FGA,FGG Melatonin Degradation I CYP2D6,CYP1A2,CYP4B1,CYP2C18 Superpathway of Melatonin Degradation CYP2D6,CYP1A2,CYP4B1,CYP2C18 IL-12 Signaling and Production in Macrophages ALB,AKT2,APOB,APOC3,APOF,SERPINA1,REL CXCR4 Signaling ROCK2,AKT2,ADCY4,GNA11,GNB5,MYL4,GNB1L,GNG7 TCA Cycle II (Eukaryotic) CS,ACO2,MDH2 Genes

21 Gluconeogenesis I GPI,ALDOB,MDH2 Thrombin Signaling ROCK2,AKT2,ADCY4,GNA11,GNB5,MYL4,ARHGEF1,GNB1L,GNG7 Telomerase Signaling ETS1,AKT2,ABL1,ETS2,ELK3,HDAC5 Cardiac β-adrenergic Signaling PDE2A,ADCY4,GNB5,GNB1L,PPP1CA,GNG7,AKAP11 Intrinsic Prothrombin Activation Pathway FGB,FGA,FGG Relaxin Signaling PDE2A,AKT2,ADCY4,GNA11,GNB5,GNB1L,GNG7 Sphingosine-phosphate Signaling S1PR3,AKT2,ADCY4,CASP1,PDGFB,ASAH1 EPHB4,AKT2,GNA11,GNB5,ABL1,GIT1,PDGFB,GNG7,ROCK2,FZD4,SDCBP,MYL4,CHMP1A,GN Axonal Guidance Signaling B1L,RASA1 Production of Nitric Oxide and Reactive Oxygen Species in Macrophages ALB,AKT2,APOB,APOC3,APOF,CAT,SERPINA1,PPP1CA α-adrenergic Signaling GYS1,ADCY4,GNB5,GNB1L,GNG7 Gαq Signaling ROCK2,AKT2,GYS1,GNA11,GNB5,GNB1L,GNG7 FXR/RXR Activation AKT2,MLXIPL,APOB,APOC3,FETUB Huntington's Disease Signaling AKT2,ATP5B,GNA11,CASP1,GNB5,GNB1L,RASA1,GNG7,HDAC5 NAD biosynthesis II (from tryptophan) TDO2,ABL1 Chondroitin Sulfate Degradation (Metazoa) CD44,ARSB Gα12/13 Signaling ROCK2,AKT2,CDH5,MYL4,ARHGEF1,RASA1 G Beta Gamma Signaling AKT2,GNA11,GNB5,GNB1L,GNG7 Gαi Signaling S1PR3,APLNR,ADCY4,GNB5,GNB1L,GNG7 CCR5 Signaling in Macrophages CCR5,GNB5,GNB1L,GNG7 Leukocyte Extravasation Signaling ROCK2,F11R,CDH5,CD44,ABL1,VCL,MMP24,MMP12 Breast Cancer Regulation by Stathmin ROCK2,CCNE2,ADCY4,GNB5,ARHGEF1,GNB1L,PPP1CA,GNG7 Retinol Biosynthesis Ces1b/Ces1c,LIPE,PNPLA2 IL-1 Signaling ADCY4,GNA11,GNB5,GNB1L,GNG7 Methionine Degradation I (to Homocysteine) SUV39H2,MAT1A

22 Docosahexaenoic Acid (DHA) Signaling AKT2,BCL2A1,PNPLA2 Acute Phase Response Signaling ALB,AKT2,APOH,SERPINA1,FGB,FGA,FGG Insulin Receptor Signaling AKT2,GYS1,LIPE,IRS2,VAMP2,PPP1CA Ethanol Degradation IV CAT,ACSS2 Cysteine Biosynthesis III (mammalia) SUV39H2,MAT1A DNA damage-induced σ Signaling CCNE2,AKT2 Pathway p-value # Genes Liver Genes Nur77 Signaling in T Lymphocytes CASP9,HDAC2,CYCS,MEF2D,CHP1,FCER1G,NFATC1,PPP3CC Antigen Presentation Pathway HLA-C,HLA-B,CD74,TAP1,TAPBP,MR1 Complement System CFD,SERPING1,MASP2,C4B (includes others),c1qc,c3ar1 Spermine Biosynthesis SMS,AMD1 Protein Ubiquitination Pathway UCHL3,DNAJB4,UBE2L3,CUL1,DNAJC19,DNAJB9,DNAJB14,TAP1,DNAJC21,PAN2,PSMC6,CUL 2,HLA-C,PSMD12,USP16,HLA-B,USP46,SUGT1,DNAJB1 Spermidine Biosynthesis I SMS,AMD1 Role of PKR in Interferon Induction and Antiviral Response IKBKB,CASP9,CYCS,TAB2,NFKB2,IRF1 LXR/RXR Activation KNG1,PON1,ITIH4,SAA1,VTN,MYLIP,CLU,C4B (includes others),pltp,nfkb2,il1rap Assembly of RNA Polymerase II Complex TAF9,CCNH,CDK7,DR1,TAF9B,POLR2K Bile Acid Biosynthesis, Neutral Pathway BAAT,CYP27A1,AKR1C4 Methylglyoxal Degradation III Akr1b10,AKR1C4,AKR1B1 Melatonin Degradation I Cyp2c40 (includes others),ugt2b28,ugt2b15,cyp2c18,sult1d1 icos-icosl Signaling in T Helper Cells GAB2,SHC1,IKBKB,CHP1,FCER1G,NFATC1,PPP3CC,NFKB2,INPP5D

23 Type I Diabetes Mellitus Signaling IKBKB,CASP9,CYCS,HLA-C,HLA-B,FCER1G,NFKB2,IL1RAP,IRF1 Superpathway of Melatonin Degradation Cyp2c40 (includes others),ugt2b28,ugt2b15,cyp2c18,sult1d1 Thyroid Hormone Metabolism II (via Conjugation and/or Degradation) UGT2B28,UGT2B15,Sult1d1 Systemic Lupus Erythematosus Signaling KNG1,RNU12,SNRPE,HLA-C,RNU2-1,CREM,HLA-B,FCER1G,ZCRB1,NFATC1,HNRNPC,INPP5D Tryptophan Degradation to 2-amino- 3-carboxymuconate Semialdehyde TDO2,HAAO Mitochondrial Dysfunction NDUFA5,COX7A2,CASP9,CYCS,COX6C,NDUFB4,NDUFB6,UQCRB,GPX4,NDUFS4 Role of JAK2 in Hormone-like Cytokine Signaling SH2B3,SHC1,EPOR,SIRPA Cytotoxic T Lymphocyte-mediated Apoptosis of Target Cells CASP9,CYCS,HLA-C,HLA-B,FCER1G Asparagine Degradation I ASPG L-cysteine Degradation II CTH TWEAK Signaling IKBKB,CASP9,CYCS,NFKB2 Mineralocorticoid Biosynthesis HSD3B2,Cyp2d22 UDP-N-acetyl-D-galactosamine Biosynthesis II GNPNAT1,GNPDA1 Pathway p-value # Genes Skeletal Muscle Hypoxia Signaling in the Cardiovascular System UBE2A,SUMO1,UBE2V2,HIF1A,NOS3,UBE2I Selenocysteine Biosynthesis II (Archaea and Eukaryotes) SEPHS2,PSTK UDP-N-acetyl-D-galactosamine Biosynthesis II GNPNAT1,GNPDA2 Genes

24 Folate Transformations I MTHFS,MTHFR RhoGDI Signaling ROCK2,ARHGAP5,MYL9,GNAI3,CDH4,RHOB,ARPC5,GDI2,RHOJ,GNG5 Glutamate Removal from Folates GGH Xanthine and Xanthosine Salvage PNP CXCR4 Signaling ROCK2,MYL9,GNAI3,FOS,RHOB,ADCY4,MAPK8,RHOJ,GNG5 Glucocorticoid Receptor Signaling CCNH,SGK1,MAPK8,BGLAP,TBP,GTF2E2,TAF7,CD163,FOS,DUSP1,SUMO1,CHUK,UBE2I Sphingosine-phosphate Signaling PLCD3,GNAI3,CASP12,RHOB,ADCY4,RHOJ,CASP8 Cell Cycle Control of Chromosomal Replication ORC2,RPA3,ORC4 Assembly of RNA Polymerase II Complex CCNH,TBP,GTF2E2,TAF7 Pathway p-value # Genes D-myo-inositol (1,4,5,6)- Tetrakisphosphate Biosynthesis TNS3,NUDT11,PPP1R12A,ILKAP,PTEN,NUDT1 D-myo-inositol (3,4,5,6)- tetrakisphosphate Biosynthesis TNS3,NUDT11,PPP1R12A,ILKAP,PTEN,NUDT1 D-myo-inositol-5-phosphate Metabolism TNS3,NUDT11,PPP1R12A,ILKAP,PTEN,NUDT1 3-phosphoinositide Degradation TNS3,NUDT11,PPP1R12A,ILKAP,PTEN,NUDT1 3-phosphoinositide Biosynthesis TNS3,NUDT11,PPP1R12A,ILKAP,PTEN,NUDT1 Superpathway of Inositol Phosphate Compounds TNS3,NUDT11,PPP1R12A,ILKAP,PTEN,NUDT1 Lipoate Biosynthesis and Incorporation II LIAS Role of Hypercytokinemia/hyperchemokine mia in the Pathogenesis of Influenza IL1B,IFNA1/IFNA13 Pancreatic Islets Genes

25 Systemic Lupus Erythematosus Signaling AKT2,SNRPB2,IL1B,IFNA1/IFNA13 Oxidized GTP and dgtp Detoxification NUDT1 L-serine Degradation SDSL EIF2 Signaling AKT2,RPL30,RPL12,RPSA Role of Cytokines in Mediating Communication between Immune Cells IL1B,IFNA1/IFNA13 Docosahexaenoic Acid (DHA) Signaling AKT2,IL1B ILK Signaling AKT2,PPP1R12A,ILKAP,PTEN Melanoma Signaling AKT2,PTEN Role of Tissue Factor in Cancer AKT2,IL1B,PTEN Integrin Signaling AKT2,PPP1R12A,ILKAP,PTEN Role of PI3K/AKT Signaling in the Pathogenesis of Influenza AKT2,IFNA1/IFNA13 Endometrial Cancer Signaling AKT2,PTEN TREM1 Signaling AKT2,IL1B PI3K Signaling in B Lymphocytes CD81,AKT2,PTEN Cardiac β-adrenergic Signaling PPP1R12A,GNG4,AKAP11 Insulin Receptor Signaling AKT2,PPP1R12A,PTEN