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| Cluster | Biological process | Genes |
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| Activation of immune system | Cd55 Daf2 Fcer1g Klre1 Klrk1 Lax1 Lyn Malt1 Masp2 Plcg2 Tlr3 Tlr4 Tlr6 Unc93b1 |
| Adaptive immune response | Bcl3 Cd55 Cd74 Daf2 Fcer1g Fcgr3 Icam1 Icosl Lilrb3 Masp2 Pou2f2 Slc11a1 Tlr6 |
| Cell activation | Bank1 Bcl11a Bcl3 Btk Casp1 Cd74 Clcf1 Cplx2 Cxcr5 Elf4 Entpd1 Fcer1g Fcgr3 Fyb Gapt Gpr183 H2-M3 Hdac9 Hhex Icosl Il4 Irf1 Irf4 Itgax Klre1 Klrk1 Lax1 Lbp Lilrb3 Lyn Malt1 Plcg2 Pou2f2 Slc11a1 Tlr3 Tlr4 Tlr6 Vwf |
| Defense response | Alox5 Bcl3 Btk Ccl19 Ccl5 Ccr2 Ccr5 Cd163 Cd180 Cd36 Cd55 Cd74 Chst2 Ciita Clec4a2 Clec4d Cnr2 Daf2 Ddx58 Fcer1g Fcgr3 H2-K1 H2-M3 Hdac9 Il18rap Il1b Irf8 Lbp Lta Ly86 Lyn Malt1 Masp2 Mefv Ncf1 Neurod2 Pglyrp1 Prg2 Samhd1 Slc11a1 Tirap Tlr3 Tlr4 Tlr6 |
| I-kappa8 kinase/NF-kappa8 cascade | Btk Irak2 Malt1 Rel Tirap Tlr4 |
| 1 | Immune effector process | Bcl3 Btk Cd55 Cd74 Cplx2 Daf2 Fcer1g Fcgr3 Icam1 Icosl Lax1 Lbp Lilrb3 Lyn Masp2 Ncf1 Pou2f2 Slc11a1 |
| Immune response | Bcl3 Btk Ccl19 Ccl5 Ccl9 Ccr2 Cd180 Cd55 Cd74 Ciita Clec4a2 Clec4d Cplx2 Daf2 Ddx58 Enpp1 Fasl Fcer1g Fcgr3 Fcgrt Gpr183 H2-D1 H2-K1 H2-M3 H2-Q10 H2-Q2 H2-Q7 H2-Q8 H2-T23 Hfe Icam1 Icosl Igj Il18rap Il1b Il4 Irf8 Irf8 Lax1 Lbp Lilrb3 Lta Ltb Ly86 Lyn Malt1 Masp2 Ncf1 Oas1b Pglyrp1 Plcg2 Pou2f2 Prg2 Samhd1 Slc11a1 Tirap Tlr3 Tlr4 Tlr6 |
| Immune response-activating signal transduction | Fcer1g Klre1 Klrk1 Lax1 Lyn Malt1 Plcg2 Tlr3 Tlr4 Tlr6 Unc93b1 |
| Immune system process | Bank1 Bcl11a Bcl3 Btk Casp1 Ccl19 Ccl5 Ccl9 Ccr2 Cd180 Cd300lf Cd55 Cd74 Ciita Clcf1 Clec4a2 Clec4d Cplx2 Crkl Csf1 Csf3r Cxcr5 Daf2 Ddx58 Dnase2a Elf4 Enpp1 Fasl Fcer1g Fcgr3 Fcgrt Fyb Gapt Gpr183 H2-D1 H2-K1 H2-M3 H2-Q10 H2-Q2 H2-Q7 H2-Q8 H2-T23 Hdac9 Hfe Hhex Icam1 Icosl Igj Il18rap Il1b Il4 Irf1 Irf4 Irf8 Itgax Klre1 Klrk1 Lax1 Lbp Lilrb3 Lta Ltb Ly86 Lyn Malt1 Masp2 Myo1e Ncf1 Oas1b Pglyrp1 Plcg2 Pou2f2 Prg2 Samhd1 Slc11a1 Terc Tirap Tlr3 Tlr4 Tlr6 Tnfrsf13c Unc93b1 |
| Inflammatory response | Alox5 Btk Ccl19 Ccl5 Ccr2 Cd163 Cd180 Cd55 Chst2 Cnr2 Daf2 Fcgr3 Hdac9 Il1b Lbp Lta Ly86 Lyn Masp2 Mefv Ncf1 Slc11a1 Tirap Tlr3 Tlr4 Tlr6 |
| Lymphocyte activation | Bank1 Bcl11a Bcl3 Cd74 Clcf1 Cxcr5 Elf4 Gapt Gpr183 H2-M3 Hdac9 Hhex Icosl Il4 Irf1 Itgax Klre1 Klrk1 Lax1 Malt1 Plcg2 Pou2f2 Slc11a1 |
| Lymphocyte activation during immune response | Bcl3 Gpr183 H2-M3 Plcg2 Slc11a1 |
| Lymphocyte mediated immunity | Bcl3 Cd55 Cd74 Daf2 Fcer1g Fcgr3 Icam1 Icosl Lilrb3 Masp2 Pou2f2 Slc11a1 |
| Positive regulation of interferon-gamma production | Bcl3 H2-M3 Irf8 Klre1 Klrk1 Lta Slc11a1 Tlr4 |
| Regulation of defense response | Adrb2 Anxa1 Cadm1 Ccl5 Ccr5 Cnr2 Crtam Fcer1g Fcgr3 H2-Bl H2-M3 Klrb1b Klre1 Klrk1 Lta Nt5e Tgm2 Tlr3 Tlr4 Tlr6 Unc93b1 |
| Regulation of immune effector process | Cadm1 Crtam Fcer1g Fcgr3 H2-Bl H2-K1 H2-M3 Hmox1 Klrb1b Klre1 Klrk1 Lta |
| Regulation of immune response | Btla Cadm1 Cd55 Crtam Daf2 Fcer1g Fcgr3 H2-Bl H2-K1 H2-M3 Il4 Klrb1b Klre1 Klrk1 Lax1 Lta Lyn Malt1 Masp2 Plcg2 Slc11a1 Tlr3 Tlr4 Tlr6 Tnfrsf13c Unc93b1 |
| Regulation of inflammatory response | Adrb2 Anxa1 Ccl5 Cnr2 Fcer1g Fcgr3 Lta Nt5e Tgm2 Tlr4 |
| Regulation of leucocyte mediated cytotoxicity | Cadm1 Crtam H2-Bl H2-K1 H2-M3 Klrb1b Klre1 Klrk1 |
| Apoptosis | Actc1 Bag3 Dapl1 Dedd2 Fasl Gramd4 Hipk2 Nfkb1 Nod1 Pea15a Pim2 Pmaip1 Psen2 Ripk1 Sgk1 Sgms1 Shisa5 Tmem173 Traf1 Traf3ip2 Traf5 |
| Immune response | B2m Ccl3 Ccl5 Cxcl9 Eomes Fasl Foxp3 H2-Q10 Il18r1 Il1rl1 Il7r Irgm1 Myo1f Pf4 Psen2 Tgtp1 Tlr1 Tmem173 Tnfaip8l2 Tnfsf8 Traf3ip2 |
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| 2 | Immune system process | B2m Ccl3 Ccl5 Cxcl9 Eomes Fasl Flt3l Foxp3 Gimap5 H2-Q10 Il18r1 Il1rl1 Il2rb Il7r Irf1 Irgm1 Jak3 Myo1f Nfkb1 P2rx7 Pf4 Pik3cd Psen2 Slamf1 Tgfbr2 Tgtp1 Tlr1 Tmem173 Tnfaip8l2 Tnfsf8 Traf3ip2 |
| Regulation of I-kappaB kinase/NF-kappaB cascade | Card6 Il1rl1 Nod1 Pim2 Tgm2 |
| Regulation of signal transduction | Arhgef12 Arhgef3 Arrb1 Arrb2 Axin2 Card6 Cd44 Fasl Furin Il1rl1 Nod1 P2rx7 Pim2 Psen2 Rasa3 Rasgrp2 Rgs11 Runx2 S1pr1 Smad7 Socs3 Spry2 Tgm2 Zeb2 |
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| 3 | Immune system process | Add2 Ahsp Ank1 Ccl4 Ccr2 Cd48 Cebpa Ctla4 Ctse Elane Epas1 Epb4.2 Gimap5 Gm5077 Id2 Ifng Il1r1 Il1rl1 Il1rl2 Itgam Junb Klf1 Klf11 Mpo Plscr1 Polr3c Samhd1 Spna1 Tal1 Tgtp1 Trim10 Txnrd2 Zbtb32 |
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| 4 | Cell communication | Atg16l1 Bmp8a Cacna1c Cblc Chat Cldn5 Cxcr7 Drd5 Erbb3 Gad1 Gad2 Gast Gja5 Gnal Gpr12 Gpr173 Gpr82 Grp Grpr Hnf1b Itgax Kcnk2 Lin7a Mrgprb2 Ngfr Olfr1010 Olfr1022 Olfr1048 Olfr107 Olfr1090 Olfr1115 Olfr1161 Olfr128 Olfr1377 Olfr1384 Olfr1388 Olfr1459 Olfr1462 Olfr1469 Olfr1495 Olfr304 Olfr33 Olfr350 Olfr365 Olfr516 Olfr523 Olfr556 Olfr606 Olfr62 Olfr651 Olfr68 Olfr684 Olfr724 Olfr768 Olfr770 Olfr784 Olfr790 Olfr796 Olfr845 Olfr889 Olfr904 Olfr924 Olfr974 Park2 Pdx1 Pik3c2g Plat Pth Rab3b Rab3c Slc1a2 Slc6a4 Syn2 Taar4 Tacr1 Upk1a Vmn2r26 Vmn2r81 Xcr1 |
| G-protein coupled receptor protein signaling pathway | Cxcr7 Drd5 Gast Gnal Gpr12 Gpr173 Gpr82 Grp Grpr Kcnk2 Mrgprb2 Olfr1010 Olfr1022 Olfr1048 Olfr107 Olfr1090 Olfr1115 Olfr1161 Olfr128 Olfr1377 Olfr1384 Olfr1388 Olfr1459 Olfr1462 Olfr1469 Olfr1495 Olfr304 Olfr33 Olfr350 Olfr365 Olfr516 Olfr523 Olfr556 Olfr606 Olfr62 Olfr651 Olfr68 Olfr684 Olfr724 Olfr768 Olfr770 Olfr784 Olfr790 Olfr796 Olfr845 Olfr889 Olfr904 Olfr924 Olfr974 Pth Taar4 Tacr1 Vmn2r26 Vmn2r81 Xcr1 |
| Signal transduction | Bmp8a Cblc Cxcr7 Drd5 Erbb3 Gast Gnal Gpr12 Gpr173 Gpr82 Grp Grpr Itgax Kcnk2 Mrgprb2 Ngfr Olfr1010 Olfr1022 Olfr1048 Olfr107 Olfr1090 Olfr1115 Olfr1161 Olfr128 Olfr1377 Olfr1384 Olfr1388 Olfr1459 Olfr1462 Olfr1469 Olfr1495 Olfr304 Olfr33 Olfr350 Olfr365 Olfr516 Olfr523 Olfr556 Olfr606 Olfr62 Olfr651 Olfr68 Olfr684 Olfr724 Olfr768 Olfr770 Olfr784 Olfr790 Olfr796 Olfr845 Olfr889 Olfr904 Olfr924 Olfr974 Pdx1 Pik3c2g Plat Pth Rab3b Rab3c Taar4 Tacr1 Upk1a Vmn2r26 Vmn2r81 Xcr1 |
| Apoptosis, apoptosis regulation | Alms1 Bcl2l1 Birc5 Bub1 Bub1b Casp6 Ckap2 Cul7 E2f1 E2f2 Egln3 Epha2 Fas Ift57 Krt18 Krt8 Lig4 Phlda1 Rad21 Rtn3 Stk3 Tfdp1 Tia1 Tpx2 Traf4 Trp53inp1 Vdac1 |
| Cell activation | Ada Bcl11b Ccnd3 Cd4 Cd8a Cxcl12 Fas Hdac7 Hells Lig4 Ly6d Msh6 Patz1 Rag1 Rorc Satb1 Sox4 Themis |
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| 5 | Cell cycle | 1190002H23Rik Anapc5 Anln Aspm Aurka B230120H23Rik Birc5 Bub1 Bub1b C79407 Casc5 Ccdc99 Ccna2 Ccnb1 Ccnb2 Ccnd3 Ccne2 Ccnf Ccng2 Cdc20 Cdc25a Cdc25c Cdc45 Cdca2 Cdca3 Cdca5 Cdk1 Cdkn1a Cdkn2c Cdkn3 Cenpe Cenpj Cep55 Chek1 Ckap2 Ckap5 Cul7 E2f1 E2f2 E2f3 E2f7 Ercc6l Esco2 Espl1 F630043A04Rik Fam33a Fbxo5 Gas2l3 Gsg2 H2afx Haus2 Hells Kif11 Kif2c Kifc1 Lig4 Mad1l1 Mki67 Myb Ncapd2 Ncaph Ndc80 Nde1 Nek2 Nsl1 Nuf2 Nusap1 Pard6g Phgdh Prc1 Psrc1 Pttg1 Rad21 Rad51c Rbbp4 Rcc1 Sgol1 Sgol2 Skp2 Spag5 Spc25 Stmn1 Tacc2 Tacc3 Tfdp1 Tpx2 Trp53inp1 Tubb5 Tubg1 Ube2c Uhrf1 Wee1 |
| Cell proliferation | Alms1 Aspm Bcl2l1 Ccnd3 Cxcl12 Gins1 Hells Hmgb1 Lig4 Lipa Mki67 Ncapg2 Nde1 Satb1 Tacc2 Tacc3 Uhrf1 Vegfa |
| Lymphocyte activation | Ada Bcl11b Ccnd3 Cd4 Cd8a Cxcl12 Faz Hdac7 Hells Lig4 Ly6d Msh6 Patz1 Rag1 Rorc Satb1 Sox4 Themis |
| Lymphocyte differentiation | Ada Bcl11b Cd4 Cd8a Fas Hdac7 Hells Lig4 Ly6d Patz1 Rag1 Rorc Satb1 Sox4 Themis |
| T-cell activation | Bcl11b Ccnd3 Cd4 Cd8a Cxcl12 Fas Lig4 Patz1 Rag1 Rorc Satb1 Sox4 Themis |
| T-cell differentiation | Bcl11b Cd4 Cd8a Fas Lig4 Patz1 Rag1 Rorc Satb1 Sox4 Themis |
| V(D)J recombination | Bcl11b Lig4 Rag1 Xrcc6 |
| CD8-positive, alpha-beta T-cell differentiation | Pax1 Satb1 |
| Cell differentiation | Acan Bcl11b Bcl2l1 Bcl6 Bmp7 Cby1 Cdkn1c Cux1 Cxcl12 Dyrk1b Ephb2 Gjc1 Gpc2 Hdac2 Id3 Ift81 Igfbp3 Lhx2 Lig4 Morc1 Msi2 Myh10 Notch1 Notch3 Ntn1 Paqr5 Pax1 Pias2 Pitx2 Ptprf Rag1 Rag2 Runx1 Satb1 Sox11 Spata6 Spo11 Stra8 Tbata Thy1 Whrn |
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| 6 | Cell-cell adhesion | Acan Arvcf Jup Lmo4 Mcam Ncam1 Ntn1 Ptprf Pvrl3 Vangl2 |
| Lymphocyte differentiation | Bcl11b Bcl6 Lig4 Pax1 Rag1 Rag2 Satb1 |
| Somatic diversification and recombination of T-cell receptor genes | Bcl11b Lig4 |
| T-cell activation | Bcl11b Cxcl12 Lig4 Pax1 Rag1 Rag2 Satb1 Sla2 |
| T-cell differentiation | Bcl11b Lig4 Pax1 Rag1 Rag2 Satb1 |
| T-cell receptor V(D)J recombination | Bcl11b Lig4 |
| V(D)J recombination | Bcl11b Lig4 Rag1 Rag2 |
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