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Supplemental Figure 1. Protein-Protein Interaction Network with Increased Expression in Fteb During the Luteal Phase

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Supplemental Figure 1. Protein-Protein Interaction Network with Increased Expression in Fteb During the Luteal Phase Supplemental Figure 1. Protein-protein interaction network with increased expression in FTEb during the luteal phase. Supplemental Figure 2. Protein-protein interaction network with decreased expression in FTEb during luteal phase. LEGENDS TO SUPPLEMENTAL FIGURES Supplemental Figure 1. Protein-protein interaction network with increased expression in FTEb during the luteal phase. Submission of probe sets differentially expressed in the FTEb specimens that clustered with SerCa as well as those specifically altered in FTEb luteal samples to the online I2D database revealed overlapping networks of proteins with increased expression in the four FTEb samples and/or FTEb luteal samples overall. Proteins are represented by nodes, and known and predicted first-degree interactions are represented by solid lines. Genes encoding proteins shown as large ovals highlighted in blue were exclusively found in the first comparison (Manuscript Figure 2), whereas those highlighted in red were only found in the second comparison (Manuscript Figure 3). Genes encoding proteins shown as large ovals highlighted in black were found in both comparisons. The color of each node indicates the ontology of the corresponding protein as determined by the Online Predicted Human Interaction Database (OPHID) link with the NAViGaTOR software. Supplemental Figure 2. Protein-protein interaction network with decreased expression in FTEb during the luteal phase. Submission of probe sets differentially expressed in the FTEb specimens that clustered with SerCa as well as those specifically altered in FTEb luteal samples to the online I2D database revealed overlapping networks of proteins with decreased expression in the four FTEb samples and/or FTEb luteal samples overall. Proteins are represented by nodes, and known and predicted first-degree interactions are represented by solid lines. Genes encoding proteins shown as large ovals highlighted in blue were exclusively found in the first comparison (Manuscript Figure 2), whereas those highlighted in red were only found in the second comparison (Manuscript Figure 3). Genes encoding proteins shown as large ovals highlighted in black were found in both comparisons. The color of each node indicates the ontology of the corresponding protein as determined by the Online Predicted Human Interaction Database (OPHID) link with the NAViGaTOR software. Supplemental Table 1. Genes differentially expressed in subset of FTEb samples. Probe Set ID Gene Title Symbol Fold Change* q-value** Regulation of Transcription (106) androgen receptor (dihydrotestosterone receptor; testicular feminization; spinal and bulbar muscular atrophy; Kennedy 211110_s_at disease) AR 0.2 3.7 202820_at aryl hydrocarbon receptor AHR 2.7 1.9 225490_at AT rich interactive domain 2 (ARID RFX-like) ARID2 0.7 3.5 212614_at †AT rich interactive domain 5B (MRF1-like) ARID5B 3.0 1.0 228890_at atonal homolog 8 (Drosophila) ATOH8 3.0 3.7 221530_s_at basic helix-loop-helix domain containing class B 3 BHLHB3 0.5 3.7 223185_s_at basic helix-loop-helix domain containing class B 3 BHLHB3 0.3 2.0 203543_s_at basic transcription element binding protein 1 BTEB1 2.8 3.1 220272_at basonuclin 2 BNC2 0.4 3.7 230722_at basonuclin 2 BNC2 0.3 3.7 222891_s_at B-cell CLL/lymphoma 11A (zinc finger protein) BCL11A 0.3 1.0 203140_at B-cell CLL/lymphoma 6 (zinc finger protein 51) BCL6 2.9 0.0 215990_s_at B-cell CLL/lymphoma 6 (zinc finger protein 51) BCL6 4.7 3.5 BTB and CNC homology 1 basic leucine zipper transcription 204194_at factor 1 BACH1 2.2 2.7 BTB and CNC homology 1, basic leucine zipper 236796_at transcription factor 2 BACH2 8.2 3.7 218384_at calcium regulated heat stable protein 1 24kDa CARHSP1 2.5 0.0 224910_at calcium regulated heat stable protein 1 24kDa CARHSP1 2.2 3.7 1555370_a_at calmodulin binding transcription activator 1 CAMTA1 5.2 1.0 213268_at calmodulin binding transcription activator 1 CAMTA1 7.2 2.7 209967_s_at cAMP responsive element modulator CREM 3.9 3.7 214508_x_at cAMP responsive element modulator CREM 2.2 3.7 212501_at §CCAAT/enhancer binding protein (C/EBP) beta CEBPB 3.6 1.3 203973_s_at CCAAT/enhancer binding protein (C/EBP) delta CEBPD 3.6 2.1 213006_at CCAAT/enhancer binding protein (C/EBP) delta CEBPD 6.0 2.1 213003_s_at CCAAT/enhancer binding protein (C/EBP), delta CEBPD 3.8 3.1 1561181_at CDNA FLJ31194 fis clone KIDNE2000510 --- 4.1 1.3 202575_at cellular retinoic acid binding protein 2 CRABP2 0.2 3.5 235791_x_at chromodomain helicase DNA binding protein 1 CHD1 1.5 3.7 1562673_at Clone IMAGE:5286598 mRNA --- 3.1 2.1 201160_s_at †cold shock domain protein A CSDA 1.4 3.1 1555411_a_at cyclin L1 CCNL1 2.3 0.0 220046_s_at cyclin L1 CCNL1 2.2 0.0 E74-like factor 3 (ets domain transcription factor 201510_at epithelial-specific ) ELF3 3.4 1.9 E74-like factor 3 (ets domain transcription factor epithelial- 210827_s_at specific ) ELF3 3.1 3.7 226099_at ‡elongation factor RNA polymerase II 2 ELL2 2.9 2.1 226982_at ‡elongation factor RNA polymerase II 2 ELL2 3.5 3.5 219517_at elongation factor RNA polymerase II-like 3 ELL3 0.4 2.0 221950_at empty spiracles homolog 2 (Drosophila) EMX2 0.5 1.1 200878_at endothelial PAS domain protein 1 EPAS1 2.7 4.3 Probe Set ID Gene Title Symbol Fold Change* q-value** 225645_at ets homologous factor EHF 0.5 0.7 241397_at Ets homologous factor EHF 0.3 1.1 212024_x_at ‡flightless I homolog (Drosophila) FLII 1.4 2.7 202949_s_at ± four and a half LIM domains 2 FHL2 4.0 3.7 227613_at Full length insert cDNA clone YZ93G08 --- 4.1 2.7 226446_at hairy and enhancer of split 6 (Drosophila) HES6 0.3 4.3 204225_at histone deacetylase 4 HDAC4 2.3 3.5 206194_at homeo box C4 HOXC4 0.4 3.7 211597_s_at homeodomain-only protein /// homeodomain-only protein HOP 6.0 3.7 218068_s_at hypothetical protein FLJ22301 FLJ22301 2.1 4.3 LOC148203 /// hypothetical protein LOC148203 /// similar to hypothetical LOC115648 /// 240155_x_at protein FLJ13659 /// zinc finger protein 493 ZNF493 0.6 1.1 ±,‡,§inhibitor of DNA binding 2 dominant negative helix-loop- 201565_s_at helix protein ID2 2.4 1.2 ‡,§inhibitor of DNA binding 2 dominant negative helix-loop- 201566_x_at helix protein ID2 2.2 3.5 ±,§inhibitor of DNA binding 2 dominant negative helix-loop- 213931_at helix protein ID2 2.9 1.5 206332_s_at interferon gamma-inducible protein 16 IFI16 2.8 1.0 208966_x_at interferon gamma-inducible protein 16 IFI16 2.8 2.1 204785_x_at interferon (alpha beta and omega) receptor 2 IFNAR2 1.8 3.7 204786_s_at interferon (alpha beta and omega) receptor 2 IFNAR2 2.1 2.1 204166_at KIAA0963 KIAA0963 1.8 1.2 231015_at Kruppel-like factor 15 KLF15 2.2 1.9 212924_s_at ‡LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) LSM4 0.7 4.3 205101_at MHC class II transactivator MHC2TA 5.4 3.7 1555832_s_at MRNA; cDNA DKFZp564C2063 (from clone DKFZp564C2063) --- 1.9 2.1 232676_x_at myelin expression factor 2 MYEF2 0.5 2.1 204959_at myeloid cell nuclear differentiation antigen MNDA 2.0 2.7 220184_at Nanognuclear homeobox factor of kappa light polypeptide gene enhancer in NANOG 0.6 3.7 209239_at B-cells 1 (p105) NFKB1 1.9 2.1 225344_at nuclear receptor coactivator 7 NCOA7 6.9 0.0 nuclear receptor subfamily 3 group C member 1 201865_x_at (glucocorticoid receptor) NR3C1 1.6 3.5 202080_s_at OGT(O-Glc-NAc transferase)-interacting protein 106 KDa OIP106 0.6 4.3 227220_at ovarian zinc finger protein HOZFP 0.4 4.3 37152_at peroxisome proliferative activated receptor delta PPARD 2.5 2.1 phosphatidylinositol glycan anchor biosynthesis, class OAF /// F /// zinc finger, FYVE domain containing 20 /// OAF PIGF /// 1553569_at homolog (Drosophila) ZFYVE20 0.7 3.5 phosphatidylinositol glycan anchor biosynthesis, class OAF /// F /// zinc finger, FYVE domain containing 20 /// OAF PIGF /// 1553570_x_at homolog (Drosophila) ZFYVE20 0.7 2.7 207109_at POU domain class 2 transcription factor 3 POU2F3 4.5 1.2 203035_s_at ‡ protein inhibitor of activated STAT 3 PIAS3 0.5 4.3 202963_at regulatory factor X 5 (influences HLA class II expression) RFX5 1.7 1.2 ±runt-related transcription factor 1 (acute myeloid leukemia 209360_s_at 1; aml1 oncogene) RUNX1 2.6 0.0 1559946_s_at RuvB-like 2 (E. coli) RUVBL2 0.4 3.1 Probe Set ID Gene Title Symbol Fold Change* q-value** 206118_at signal transducer and activator of transcription 4 STAT4 3.0 3.7 225227_at ±, ‡SKI-like SKIL 2.5 2.1 201920_at †, ‡solute carrier family 20 (phosphate transporter) member 1 SLC20A1 1.8 1.0 202761_s_at spectrin repeat containing nuclear envelope 2 SYNE2 4.0 1.3 208313_s_at splicing factor 1 SF1 1.2 1.2 214633_at SRY (sex determining region Y)-box 3 SOX3 0.1 3.5 201416_at ±,‡SRY (sex determining region Y)-box 4 SOX4 0.5 3.1 215078_at superoxide dismutase 2 mitochondrial SOD2 12.7 2.1 215223_s_at superoxide dismutase 2 mitochondrial SOD2 12.3 1.9 216841_s_at superoxideSWI/SNF related dismutase matrix 2 associatedmitochondrial actin dependent SOD2 10.2 3.5 204099_at regulator of chromatin subfamily d member 3 SMARCD3 6.0 0.0 204281_at TEA domain family member 4 TEAD4 5.0 4.3 41037_at TEA domain family member 4 TEAD4 5.8 3.5 212209_at thyroid hormone receptor associated protein 2 THRAP2 1.8 3.7 236439_at Transcribed locus --- 2.7 1.2 242784_at Transcribed locus --- 3.9 1.0 243469_at Transcribed locus --- 2.1 1.2 transcription factor AP-2 gamma (activating enhancer 205286_at binding protein 2 gamma) TFAP2C 2.3 2.0 238520_at transcriptional regulating factor 1 TRERF1 0.2 3.7 ±,§v-ets erythroblastosis virus E26 oncogene homolog 201328_at 2 (avian) ETS2 4.8 1.0 ±,§v-ets erythroblastosis virus E26 oncogene homolog 201329_s_at 2 (avian) ETS2 3.5 1.2 224833_at
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