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Supplemental Material 1 Cdk20 Csrp2bp Bub1 Tmed3 1700012B15Rik Uck1 Atad2 Pbk Rfc4 Ucp3 Mtmr7 Bid Rad9 Hadh Zc3h12a Bcl2l11 1700052K11Rik Cd83 Ncaph Cdca7l Ezh2 Kif23 Rel Cdh13 Nr4a1 Pola1 Phf19 Vldlr Snx7 Fam96a Ripk2 Ccne2 Ncapd2 Pqlc3 A130009I22Rik Niacr1 Peli1 Cenpn Ralgds Dbf4 Trpc6 Gadd45b Dyrk2 Il1b Prim1 Pcna Dnmt1 Ttc30a1 Cflar Fas Tro Tank Rapgef2 Icosl 9930012K11Rik Cd28 Ccdc86 Ube2f Klhl6 Commd8 Ccrl2 D4Wsu53e Tnfaip8l2 Ehd1 Kdm2b Uhrf1 Trim37 Tecrl AI467606 Ilf2 Cobra1 Aurkb Cdc42ep2 Nfkbil2 Appbp2 Nfkbiz Zfp85-rs1 Nlrp3 Zmym5 Il6 Foxo3 Sept3 Ets2 Serpinb2 Smc3 Msh6 Itga5 Gpsm3 Slbp Dennd4c Rffl Trappc1 Mrpl34 Socs3 Ocel1 Tnfaip3 Swap70 1110003O08Rik Junb Pmm1 Cxcl10 Brca1 Acpl2 Coq10b Marcksl1 Map3k10 Braf Tnf Icam1 Pold3 AI462493 Nfkbia Dnmbp Dnajc9 Tnip1 Chfr Trim13 Slc35c2 Rb1 C78513 Limk1 C1qa Fen1 BC088983 Tsc22d3 Tnfsf9 Mapk3 E2f1 Zc3h12c Casp4 Ttf2 Maff Gmnn Zfp715 Mdm2 Mcm7 Irf1 Parp1 Ftsj2 Myo10 Irak2 Mid1ip1 Apeh Rad51c Map3k4 Tk1 E2f7 Tiparp Ptgs2 Spata13 Hmga2-ps1 Wdhd1 Clspn Ubac1 Erp29 Thap4 Dna2 Prkag2 Il1a Rfwd3 Gbp3 Cdca5 3110043O21Rik Clec4e Cxcl11 Speg Tarbp2 Cdk2 Zufsp Cdca2 E2f2 1700054N08Rik Tnfsf10 5730499H23Rik Inf2 C1qb Anapc5 Sco1 Bst2 2010107G23Rik Cnpy4 D10Wsu102e Brip1 H2-D1 Gpd1l Suv420h2 4930579G24Rik Cdc6 Cntnap2 Cyp2b10 Plod2 Irf7 C2 Lsm3 9330175E14Rik Aak1 Ick Rassf7 Cd22 Cd72 Tap1 Tcn2 Malt1 Uba7 Atp1a2 Ar Tap2 Cd86 Herc5 Heca Atp2a2 Ttc28 Dhrs3 Stat1 Ccdc22 Abca5 Nhlrc2 Ddx58 Gpx1 Dgkd Fbxl7 Lap3 Lama4 Neil1 Enpp4 Tpst1 Cybb Ccne1 Sec24d Fcgr4 Hk3 Rasgrp2 Dcun1d2 Vegfa Ecsit Ddx60 Eif2ak2 Cyp2r1 Gimap4 Fip1l1 Adar Lcp2 Mcm4 1110012J17Rik Sav1 Lrrc20 Sgk2 Nfkb2 BB236558 Nrp2 Birc2 4930558J22Rik Skp2 5830437K03Rik Kif22 Nfkb1 Slc2a6 Traf2 Ccl3 Tbc1d9 Dlx3 4833427F10Rik Lat2 Klrg1 Ddi2 Abtb2 Relb Ptprj Msc 1700049G17Rik Mcm5 Txnrd3 Cd40 D15Ertd55e Jarid2 Jak2 Depdc7 Cxcl5 Epor Foxred2 Stat4 Cebpa Krtap10-4 Ncapg 2210021J22Rik Ch25h Cdt1 Racgap1 Acadm Rnf187 Ftsjd2 Twist2 Mcm3 B3gnt8 Psrc1 Lss Tmem33 Btg2 Gkap1 Mki67 Ralgapa1 Hspa8 Atp8b4 Gm5817 Plk1 Asz1 Rnf157 Tpd52l2 Sc4mol Hiat1 Hccs Ldlr Stat3 Foxo1 Foxm1 Prepl Herpud2 BC030867 Yy1 Hmgcs1 Mapk1 Timm8b Prkci Idi1 Ermp1 Aga Ado Smad4 Aurka Cyp51 Cdc34 Rnf19b Tprgl Sgol1 Rabep1 Hmgcr Golph3l Nedd8 Hras1 Pold1 Uspl1 Chi3l3 Plin2 Wnt7a Tnfrsf1a P4ha1 Mrp63 Adm Tipin Hmox1 Stat6 Pparg Msx1 Ifnar2 Hif1a Dbp Inppl1 Eepd1 Nxph3 Acvr1b Slc2a1 Btbd6 Mcm2 Mafg Nup107 Kti12 Stk10 Haus8 Zim3 Hs6st1 Fbxw4 Xpa Nup43 Slc48a1 Impact Mapkapk2 Apc Dusp1 Set F3 Kdm6b Nhp2l1 Mars Hdac4 Pdgfb Cyfip2 Hmgb1 Bcr Itga2b Cd14 Cc2d1a Gca Bcl6 Bcl3 Atf2 Zfp36 Taf9 Stat5a Sox2 Ruvbl1 Pdlim4 Ncor1 Myc Max Hmgn2 Hdac5 Gata1 Etv6 Deaf1 Cic Trub2 Nnmt Phip D13Ertd787e Cct2 9130004C02Rik Trim3 Pdcd6 Sil1 Kdm5b Rasgef1b Mier3 Nap1l1 Itpkb Ambn Pvrl3 Chst14 Gcn1l1 Supplemental Fig. 1. Regulatory network prediction for macrophage transcriptional activation. Predicted regulatory interactions are shown as dashed lines between transcription factors (red ovals) and other genes (blue rectangles), and known interactions are depicted as solid lines. The RIKEN transcription factor database contains a number of genes that are likely or known to play only indirect roles in transcriptional regulation (e.g., modifiers of transcription such as ubiquitin ligases and kinases); these are denoted as grey ovals. Supplementary Table 1. Microarray datasets included in the present study. Database ID Pubmed ID First Author Publication Year Host Tissue Treatment GSE4712 16846716 Comer 2006 Ascites Compound GSE21117 16926395 He 2006 Ascites Bacteria GSE6785 16926388 Reece 2006 Alveolus Helminth GSE7348 17538624 Foster 2007 Bone marrow Compound GSE6376 17312158 Goodridge 2007 Bone marrow Compound GSE8621 18086374 Mages 2007 Bone marrow Compound GSE31378 17890046 Cheung 2008 Bone marrow Compound GSE4288 18230670 Kitamura 2008 Ascites Compound GSE12518 19211757 Bok 2009 Ascites Virus GSE15610 19863805 Carlson 2009 Bone marrow Compound GSE11497 19302708 Fortea 2009 Bone marrow Protozoa GSE14769 19270711 Litvak 2009 Bone marrow Compound GSE18500 20421474 Dietrich 2010 Bone marrow Bacteria E-MEXP-2554 20624948 Nguyen Hoang 2010 Ascites Protozoa GSE22935 20716764 Qualls 2010 Bone marrow Bacteria GSE19374 20123961 Rayamajh 2010 Bone marrow Bacteria GSE23306 20729857 Satoh 2010 Bone marrow Compound GSE20087 20361029 Zhang 2010 Peritoneum Compound .
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