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Network-Assisted Analysis of Primary Sjögren's Syndrome GWAS Data In Network-assisted analysis of primary Sjögren’s syndrome GWAS data in Han Chinese Kechi Fang, Kunlin Zhang, Jing Wang* Address: Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China. Email: Kechi Fang – [email protected]; Kunlin Zhang – [email protected]; Jing Wang – [email protected] *Corresponding author 1 Supplementary materials Page 3 – Page 5: Supplementary Figure S1. The direct network formed by the module genes from DAPPLE. Page 6: Supplementary Figure S2. Transcript expression heatmap. Page 7: Supplementary Figure S3. Transcript enrichment heatmap. Page 8: Supplementary Figure S4. Workflow of network-assisted analysis of pSS GWAS data to identify candidate genes. Page 9 – Page 734: Supplementary Table S1. A full list of PPI pairs involved in the node-weighted pSS interactome. Page 735 – Page 737: Supplementary Table S2. Detailed information about module genes and sigMHC-genes. Page 738: Supplementary Table S3. GO terms enriched by module genes. 2 NFKBIE CFLAR NFKB1 STAT4 JUN HSF1 CCDC90B SUMO2 STAT1 PAFAH1B3 NMI GTF2I 2e−04 CDKN2C LAMA4 8e−04 HDAC1 EED 0.002 WWOX PSMD7 0.008 TP53 PSMA1 HR 0.02 RPA1 0.08 UBC ARID3A PTTG1 0.2 TSC22D4 ERH NIF3L1 0.4 MAD2L1 DMRTB1 1 ERBB4 PRMT2 FXR2 MBL2 CBS UHRF2 PCNP VTA1 3 DNMT3B DNMT1 RBBP4 DNMT3A RFC3 DDB1 THRA CBX5 EED NR2F2 RAD9A HUS1 RFC4 DDB2 HDAC2 HCFC1 CDC45L PPP1CA MLLSMARCA2 PGR SP3 EZH2 CSNK2B HIST1H4C HIST1H4F HNRNPUL1 HR HIST4H4 TAF1C HIST1H4A ENSG00000206300 APEX1 TFDP1 RHOA ENSG00000206406 RPF2 E2F4 HIST1H4IHIST1H4B HIST1H4D HIST2H4A BRCA2 HNF4A GNL3 HDAC9 THRB ERBB2 HIST1H4EMCM4 RXRA YY1 ERCC3 CDK7 DHX30 DHX9 PEX14 PHF21A TGIF1 GRB2 GTF2H1 RUVBL1 VDR HDAC3 MAGEA2B SNORD73A GATA1 SSRP1 MTA1 TOP2A CHD1 TOP2B HIST1H4H NAP1L1 PTK2 ESR2HMGB1 MAPK12 EIF6 HIST1H4L GATA2 TRIM24 PIK3R2 RAF1 ATR SENP1 NFYA FADD HUWE1 MSH2 CDKN1A RFWD2 RB1 IL1B PTPN11 BCL3 AURKA ADAM17 MAD1L1 HMGA1 BCL6 COPS2 HTT MCM3 AR PRMT1 XRCC5 KPNA5 CHD4 HIF1A IRF2 HIST1H4K EIF3F PRKAB1 MEN1 GSTK1 PRMT2 PCNAHDAC1 MCM7 MAPK10 SIN3A RIPK2 DMRTB1 BRMS1 MTA2 MDM2MAP3K7IP2 MYL12AMNAT1 HIST1H4J ESR1SMAD2 KAT5 HSPD1 VRK1 CHD3 BLM ABL1 E2F1 RIPK1 CBS TOP1 HSPA4 DDX5 CDK5 KPNA6 MDM4 ACTG1 LRP11 NR3C1 TP53BP1 SPI1 TRAF1 NCK2 CSNK2A2 PIAS3 BCL2 SMARCA4 PHB PML TAF1B WRN SNORD21 MAD2L1BPMYL6 ENSG00000205575PRKCD NPM1SUMO1P3 NCOR2 RPA1 NFKBIB 2e−04 ETS1 HNRNPF CCND1 CITED1 C19orf50 NHP2L1 TP53BP2 STIP1 SMARCB1 ENSG00000215328 TRIP4PRIM1UBE2D3 PSME3 TAF11 UBQLN1 NEK2 FZR1 YWHAELOC100130430EP300 ERBB4 ITCHNFKBIA REL CTNNB1 8e−04 CUL3 MED17 TAF7 ATF3 MAPK11 EIF2AK2TSC22D3 CISH PIAS4 NCOR1 TSG101 FTH1 SENP2 NCOA1 JAK3 SORCS2SP1 HNRNPM CDC20 NOL3 UBE2I NCOA6 MAGEA11 RANGAP1 HSPA6 UBE2D1INCENP TRAF2IL12RB1 IL12A DAXX CDC7 0.002 SNORA62 IRF1 BUB1B PCBD1 ARID3A UBE2K CDC2 NIF3L1 TYK2 NCL CSNK2A1PXRCC1 JUN PKLR CALM3 ANAPC4 RPIA GTF2I CCNH ENSG00000206279 BAG2 DNAJA1 CSF2RB TUBB2C JAK2 ING1 PARP1 TNFRSF1A 0.008 ZBTB16 SETDB1UBE3A SKP1 STAT5B PIAS1 STAT1 TP53 ENSG00000206206 CFLAR BUB3 KCTD17 NRIP1 CREBBP RUVBL2 BCL2L1 HIST2H4B ORC1L TNIP1 GNB2L1 LOC100130702 XPC GAPDH MAPK3 CDK2 VCP ANAPC2 0.02 BRCA1STAT3 RELA CDC16 RABAC1 FXR2 HSF2 STAT4 XRCC6 XPO1 PIN1 RAD51 SORT1HSPA9 UBB PTTG1 UBE2C ERCC2C1orf25 PIAS2 STAT2 PRKDC ITGB3BP ENSG00000130041 MBIP COIL MAPK14 GSK3B HSP90AB1 CDC26ANAPC5 0.08 KRT15 ILVBL SUMO2RCOR1 MYOD1 SYK NFKB1EGR1UBC ERCC4 ENSG00000137379 COPS6 ERH RERE HSF1 EGFR MED31 TRADD MCM5IKBKB MAD2L1 FOSHMG20B COPS5SRC BMX ANAPC1 CDC27ANAPC7 CCDC85B VIM PLK1 ANAPC11 0.2 SSSCA1 KDM1 NONO CDK9 TBP TNFRSF1B VTA1 KAT2B YWHAZ NFKB2RPS27A CHUK LAMA4 SUMO4 MAPK9 RELBTUBB NOTCH1 MBL2 CCDC33 GSG2 APC TLE1 CDKN2A TXN RBX1 UBE2E1PPP1CC 0.4 ZHX1 NUDT21 SAE1 SOX10MAPKAPK5STAT5A HSPA1A CSE1LHSPA1L FBXW7 KPNB1 ENSG00000212866 PGK1 CDC23 ENSG00000183311TUBB4 UNC119 ZNF467 CEBPB DPPA2 BRD7 HSPA5 RIF1 CDKN2C CDK4 NMI EEF1A2 ANAPC10 1 MAPK8 HSPA1B IL8 IKBKGHNRNPK TRAF3 RPS27 PAFAH1B3 SH3GL2 TAF1 ENSG00000215292 NFKBIE YBX1 EEF1A1P9TRAF6 MAPK1 HSPA8 ENSG00000212860AKT1 UBE4B C1orf103 C7orf64 GTF2B PSMC1 PTP4A3 RPS7 ENSG00000185637 CDC6 UHRF2 UBE2A USP7 STUB1 TUBB2A COX17 MAPK13 HSP90AA2 RPL11 ERCC6 SUMO3 SMARCD1 POLA1 ZNF121 TSC22D4 DDX3X JMY RCHY1 POLI IGSF21NECAB2 ENSG00000205570 SMAD3 PSMD11 EEF2 SFPQ DSP RALBP1 ENSG00000206296 LOC100420759BTK SNORD55 MYC KLHL8 AURKB EEF1G PSMA2 TP73 PTEN TUBB2B SAT1 RAD23B GDF9 PRKAA2 CDC42 SLC25A5 ENSG00000206232MYO5C PLAUR TAF9 IL12B CKS2 ZNF385A KLF5 PSMD2 CALCOCO2 PPP2CA MCM6 BTRC GTF2A2 PSMA7 DLEU1 PSMA5 CSNK1A1 SF3B3 TIMM50 TDG CALM2TUBA3C KPNA1COMMD1 NGFR PSMD13 PSMB1 PSMA4 IL6 HSPBP1 CCDC90B CTPSRNF31 IKBKE CUL1 LNX1 PSMB6 TUBA3D CENPC1 HSPH1 PSMA1 RPS3 CAD VPS4B NP CPSF7 PRKCA PSME1 PSMD6 MSX1 SMAD4 BTBD2 JAK1 EIF4A1 IPO4 SERPINB9 CEPT1 CLTC TAF9BP2 WWOXTAF9BMTHFR TAF6 SPAG9 PSMD14 PSMD7 EIF2S2 PAFAH1B1 TK1 PSMC2 PSMD10 RPS20 POLR2A PSMD5 USP14 AIFM1 PAK2 ING2 CALM1 C1QBP PSMC6 FXYD6 PSMD4 STAT6 HGS POLR2B NACA FBXW11SF3B1 PSMB3 PSMD3 PCDHA4 KIAA0368 MAT1A GFPT2 PABPC1 PSMB7 PSMC4 PSMA6 RAB1A WDR33 PSMD1 PKM2 WBP2 PSMC5 PSMB4 ATXN3 PSME2 RPS11 PSMD12 SMARCC1 SYMPK PSME4 EIF5A TSC22D1 PSMB2 PSMA3 RPL13 UCHL5 PSMB8 PSMD9 PSMB10 PSMB5 ENSG00000204261 PSMF1 SF3A1 MPG TUBA4A PSMC3 PCNP ENSG00000206234 PSMD8 ENSG00000206298 4 EED HR TRIM24 PRMT2 HDAC1 DMRTB1 CBS RPA1 2e−04 ERBB4 8e−04 0.002 NIF3L1 JUN ARID3A GTF2I 0.008 TP53 STAT1 CFLAR 0.02 FXR2 STAT4 PTTG1 SUMO2 NFKB1 UBC 0.08 ERH HSF1 MAD2L1 0.2 VTA1 LAMA4 MBL2 0.4 CDKN2C NMI 1 PAFAH1B3 NFKBIE UHRF2 TSC22D4 CCDC90B PSMA1 WWOX PSMD7 PCNP 5 ES cells ES cells HSC fetal blood CD34+ CD38- HSC cord blood CD34+ CD38- HSC cord blood CD34+ CD38- CD33- HSC bone marrow CD34+ CD38- CD33- HSC fetal blood CD34+ CD38+ HSC cord blood CD34+ CD38+ stem cells HSC cord blood CD34+ CD38+ CD33- HSC periph blood CD34+ CD38+ HSC bone marrow CD34+ CD38+ HSC bone marrow CD34+ CD38+ CD33- Bone marrow CD34+ B cells cord blood CD34+ B cells Pro B cells PreI B cells PreII B cells immature B cells B cells CD19+ Tonsils Lymph node Thymus T cells cord blood CD34+ Thymic CD34+ Thymic CD34+CD38+ CD1A- Thymic CD34+CD38+ CD1A+ Thymic CD4+CD8-CD3- T cells Thymic CD4+CD8+CD3- Thymic CD4+CD8+CD3 Thymic SP CD4+ T cells Peripheral naive CD4+ T cells Th1 Th2 Thymic SP CD8+ T cells Peripheral CD8+ T cells Tonsils CD4+ T cells T cells BAFF+ T cells CD57+ T cells central memory T cells effector memory T cells gammadelta Treg NK CD56+ DC Immature DC LPS 6h Myeloid DC LPS 48h DC DC BAFF+ Myeloid CD33+ Monocyte CD14+ Derived Macrophage 16h Macrophage Macrophage LPS 4h Mast cell Mast cell IgE Spleen Blood Neutrophils RBC Whole brain Fetal brain Frontal cortex Prefrontal cortex Parietal Lobe Occipital lobe Temporal lobe Cingulate cortex Caudate nucleus Globus pallidus CNS Thalamus Subthalamic nucleus Hypothalamus Hippocampus Amygdala Cerebellum Cerebellum peduncles Pons Medulla oblongata Spinal cord Olfactory bulb Trigeminal ganglion Ciliary ganglion Dorsal root ganglion Superior cervical ganglion Adrenal gland Pituitary Thyroid Fetal thyroid Thyroid Pancreas Pancreas Skeletal muscle Tongue Muscle Smooth muscle Cardiac myocytes Cardiac muscle left ventricle Heart Heart Atrioventricular node Islet cells Islet Cells Kidney Kidney Bladder Bladder Liver Fetal liver Liver Preadipocyte subcutanous Adipocyte Adipose Lung Fetal Lung Broncho epithelial Airway Trachea Placenta Placenta Skin Skin Endothelial CD105+ Endothelial CD105+ Salivary gland Salivary Gland Esophagus Esophagus Stomach Stomach Small intestine SmallIntestine Appendix Appendix Colon Colon Ovary Ovary Uterus Uterus corpus Uterus Breast Breast Testis Testis Leydig cell Testis germ cell Testis intersitial Testis Testis seminiferous tubule Prostate Conjunctiva Conjunctiva ARID3A(205865_at) WWOX(219077_s_at) JUN(201465_s_at) TP53(211300_s_at) TRIM24(213301_x_at) JUN(213281_at) TSC22D4(208104_s_at) ZNF208(208542_x_at) GTF2IP1;LOC100093631;GTF2I(201065_s_at) GTF2IP1;LOC100093631;GTF2I(210891_s_at) CCDC90B(218288_s_at) CFLAR(214486_x_at) GTF2I(210892_s_at) CDKN2C(211792_s_at) CBS(212816_s_at) SUMO2;SUMO4(215452_x_at) SUMO2(213881_x_at) STAT1(209969_s_at) STAT4(206118_at) UBA52;RPS27A;UBB;UBC(211296_x_at) PAFAH1B3(203228_at) PTTG1(203554_x_at) MAD2L1(203362_s_at) RPA1(201529_s_at) PCNP(217816_s_at) PSMD7(201705_at) PSMA1(201676_x_at) EED(209572_s_at) HDAC1(201209_at) NMI(203964_at) NFKB1(209239_at) NIF3L1(218133_s_at) NFKBIE(203927_at) ERH(200043_at) PRMT2(221564_at) RPS27A;UBB;UBC(200633_at) RPS27A;LOC648390;UBB;UBC(217144_at) HR(220163_s_at) LAMA4(216081_at) PRMT2(210384_at) FXR2(222050_at) RPS27A;UBB;UBC(200017_at) HSF1(202344_at) ERBB4(214053_at) FXR2(35265_at) MBL2(207256_at) LAMA4(202202_s_at) 6 ES cells ES cells HSC fetal blood CD34+ CD38- HSC cord blood CD34+ CD38- HSC cord blood CD34+ CD38- CD33- HSC bone marrow CD34+ CD38- CD33- HSC fetal blood CD34+ CD38+ HSC cord blood CD34+ CD38+ stem cells HSC cord blood CD34+ CD38+ CD33- HSC periph blood CD34+ CD38+ HSC bone marrow CD34+ CD38+ HSC bone marrow CD34+ CD38+ CD33- Bone marrow CD34+ B cells cord blood CD34+ B cells Pro B cells PreI B cells PreII B cells immature B cells B cells CD19+ Tonsils Lymph node Thymus T cells cord blood CD34+ Thymic CD34+ Thymic CD34+CD38+ CD1A- Thymic CD34+CD38+ CD1A+ Thymic CD4+CD8-CD3- T cells Thymic CD4+CD8+CD3- Thymic CD4+CD8+CD3 Thymic SP CD4+ T cells Peripheral naive CD4+ T cells Th1 Th2 Thymic SP CD8+ T cells Peripheral CD8+ T cells Tonsils CD4+ T cells T cells BAFF+ T cells CD57+ T cells central memory T cells effector memory T cells gammadelta Treg NK CD56+ DC Immature DC LPS 6h Myeloid DC LPS 48h DC DC BAFF+ Myeloid CD33+ Monocyte CD14+ Derived Macrophage 16h Macrophage Macrophage LPS 4h
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