Table 2. Description of major functional clusters of coexpressed genes in mouse MPS cell samples.
| Cluster Number | Description | Representative Genes |
|---|---|---|
| 1 | MPS | Acp2, Atp6 subunits, Cd276, Cd53, Cd68, Cd84, Clec5a, Cln5/8, Csf1r, Ddx/Dhx family, Fcgr1, Gpr107/108, Hk3, lysosomal enzymes, Ifngr1/2, Il10ra, Il13ra1, Il6ra, Irak1/2, Jak1/3, Lamp1/2, Lgals8/9, M6pr, P2ry6, P2rx7, Sirpa, Tlr6/7/8, Tnfrsf11a, Cebpg, Creb3, Crebzf, Elf1, Etv5, Fli1, Foxj2, Foxn3, Foxo1, Gabpa, Hdac3/10, Hif1a, Hsf1, Klf3, Maf1, Mafg, Mitf, Nfatc1, Nfx1, Nfyc, Nr1h2, Nr2c1, Nr2f6, Nr3c1, Prdm4, Rela, Smad1/2/4, Sp3, Spi1, Srebf1, Stat6, Tcf3, Tfe3 |
| 3 | MPS | Abca1/2, Aim2, Akt2/3, Arrb1, Arrb2, Atxn7, Bak1, Cbl, Cd180, Cdk8/10/12/13/19, Csk, Ddi2, Ddx3/6/17/19a/21/23/39b/46, Dhx9/15, Grk2, H6pd, Ly9, Megf8, Mertka, Mpeg1, Naip2/5/6, Nirp1b, Ptprj, Socs4/7, Syk, Taok1/2, Traf7, Tram2, Atf1, Bach1, Bcor, Cebpa, Elf2/4, Erf, Foxk1, Foxk2, Foxo3, Foxo4, Fus, Hsf2, Ikzf1, Maf, Maz, Mef2d, Ncoa3, Ncoa6, Nfat5, Nfatc3, Nfya, Pbx2, Prdm2, Smad5 |
| 4 | Microglia and brain macrophages | Abi3, Acvr1, Adrb2, Bcl9, Bmp1/2k, Card6, Ccr5, Cd34, Csf3r, Cx3cr1, Cxxc5, Ddx31/43, Entpd1, Fcrls, Fgf13, Gabbr1, Gpr155, Gpr165, Gpr34, Hexb, Itgb3/b5, Lpcat1/2/3, Mrc2, Nckap5l, Olfml3, P2ry12/13, Paqr7, Plexna4, Nanos1, Siglech, Slc1a3/4, Slco2b1, Slc2a5, Sipa1, Tgfbr1, Tmem119, Tmem173, Trem2, Vav1, Vsir, Bhlhb9, Ebf3, Elk3, Ets1, Hivep3, Lefty1, Mef2c, Prox2, Sall1/2/3, Sox4 |
| 7 | Mitochondria and ribosome | Atp5e/g2/h/j2/l, Cox5b/6a1/6b1, Mrpl family, Nduf family, Rpl and Rps families |
| 9 | Cell cycle | Aurka, Aurkb, Birc5, Bub1, Ccna2/b1/b2/e2, Cdk1, Cenpe, Haus family, Kif family, Mcm family, Plk1, Foxm1, Mybl2 |
| 10 | Lung macrophages | Anxa2, Atxn10, Car4, Cd2, Cd200r4, Cd9, Chil3, Ctsk, Cx3Cl1, Cxcr1, F7, Fabp1, Ffar4, Flt1, Flvcr2, Gal, Htr2c, Igflr1, Il1rn, Lpl, Ly75, Nceh1, P2rx5, Plscr1, Serpine1, Siglecf, Slc6a4, Tmem138, Nlrx1, Pparg, Tcf7l2 |
| 12 | Liver KCs, peritoneal and splenic red pulp macrophages | Acp5, Adgre4, Apoc1, C6, Cd5l, Cdh5, Clec1b, Clec4f, Fabp7, Fcgr4, Il18bp, Itga9, Kcna2, Lrp5, Ly9, Pecam1, Pira1/2, Ptger1, Ptprj, Scarb1, Scarf1, Sema6d, Siglec1, Siglece, Slc11a1, Slc40a1, Slc1a2, Stab2, Tmem65, Treml4, Trpm2, Vsig4, Elk1, Id3, Nr1h3, Rxra, Smad6, Thrb, Zbtb4 |
| 13 | CCR7 DCs | Arc, Birc2, Cacnb3, Cblb, Ccl19, Ccl22, Ccr7, Cd1d1, Cd200, Cd40, Cd70, Dpp4, Fas, Icosl, Glipr2, Gpr68, Heatr9, H2-Q6/7/8/9, Il15, Il15ra, Itgb8, Laptm4b, Lrrk1, Slamf1, Socs2, Tank, Tmem19, Tnfrsf4, Tnfrsf9, Traf1, Tyk2, Vsig10, Zc3h12c, Zmynd15, Foxh1, Id2, Ikzf4, Spib, Stat4 |
| 15 | Monocytes | C3, Camkk2, Ccr2, Cd177, Cd244a, Celsr3, Clec2g, Erbb4, Fgr, Gpr15, Gpr35, Gpr141, Hpse, Il17ra, Itga4, Met, Mmp8, Ms4a4c, Nlrc5, Ptgir, Ptprc, Sell, Sgms2, Slk, Vcan, E2f2, Foxn2, Jarid2, Rara, Rfx2, Stat2b |
| 21 | Peritoneal macrophages | Ackr3, Alox15, Arg1, C4a/b, Car6, Cyp26a1, F5, F10, Fgfr1, Fzd1, Icam2, Itga6, Itgam, Jag1, Lbp, Lrg1, Mst1r, Naip1, Nt5e, Padi4, Pycard, Selp, SerpinB2, Slpi, Tgfb2, Thbs1, Wnt2, Gata6, Rarb, Smad3, Sox7, Tox2 |
| 22 | LYVE1-positive macrophages | Adam9, C3ar1, C5ar1, Cd36, Cfh, Clcn5, Ctsb, Dab2, Egfr, Epor, F13a1, Fcgrt, Frmd6, Gas6, Gpr160, Igfbp4, Lyve1, Mrc1, Nrp1, S1pr1/2, Tlr5, Tmem9, Trf, Trpv4, Etv1, Nfatc2, Tcf4 |
| 28 | DCs | Adam11, Bcl2a1b/d, Ccr6, Cd7, Clec4a4, Ddr1, Dtx1, Flt3, H2-DMb2, H2-Eb2, H2-Oa/b, Kit, Lta/b, Nlrp10, P2ry10, Siglecg, Sirpb1a, Tnfrsf18, Relb |
| 38 | Intestinal macrophages | Adam19, Asb2, Cxcl9, Cxcr4, Dna1l3, Fgl2, Gpr31b, Gpr55, Il10, Il12rb1, Kynu, Mmp9/13/14, Ocstamp, P2rx6, Pgf, Tlr12, Wnt4, Fosb, Hes1, Hic1 |
| 41 | Immediate early genes | Ccrl2, Dusp1, Mcl1, Tnfaip3, Trib1, Zfp36, Atf3, Egr1, Fos, Ier2/5, Jun, Junb, Jund, Klf2, Klf6, Nfe2l2, Nfkbiz, Tgif1 |
| 43 | LCs | Cd207, Dkk1, Dpep3, Hapin3, Il1r2, Mfge8, P2rx2, P2rx5, Plek2, Sema7a, Serpind1, Tnfaip2 |
| 49 | cDC1s | Cd8a, Clec4b2, Clnk, Ctla4, Gcsam, Gpr33, Gpr141b, Gpr171, Ildr1, Itgae, Il12b, P2ry14, Procr, Plekha5, Tlr11, Xcr1, Ncoa7 |
| 165 | Class II MHC | Cd74, H2-Aa, H2Ab1, H2-DMa/b1, H2-Eb1 |
Bold text indicates transcription factors. For descriptions and accession numbers of all genes, please see S1 Data.
Abbreviations: cDC, classical DC; DC, dendritic cell; KC, Kupffer cell; LC, Langerhans cell; MHC, major histocompatibility complex; MPS, mononuclear phagocyte system.