Table 2.
Annotation of cell-type specific co-expressed gene clusters
| Cluster ID number | Cluster profile description | Putative cluster function or cell lineage | Number transcripts | Number annotated genes | Known markers present in cluster | Significantly over-represented GO terms | Over-represented transcription factor binding sites1 |
|---|---|---|---|---|---|---|---|
| 3 | High in mast cells | Mast cell-related | 310 | 182 | Ccr1l1, Cd55, Cd200r3, Cd200r4, Cma1, Cpa3, Csf2rb2, Fcer1a, Gata2, Hrh4, Il4ra, Kit, Lif, Mcpt6, Mcpt-ps1, P2rx7, Pgr, Ptger3, Runx1 | Klf4, SPI1, SPIB, id1, Pax4, ELF5, ETS1, Myf, Eip74EF, Dof, GABPA, Broad-complex_3, TBP, SQUA, NFYA, ELK1, NFIL3,FOXD1, ABI4 | |
| 5 | High in bone marrow > mega erythroid precursors/granulocytes | Bone marrow progenitor related/granulocyte-related | 2231 | 126 | Ank1, Ccr3, Chi3l3, Cpox, Ear1, Ela2, Epb4.1, Epb4.2, Epb4.9, Epor, Epx, Eraf, Fech, Hba-a1, Hba-b1, Kel, Nfe2, Ngp, Rhag, Rhd, Urod, Uros, Xkh | GO:0030097, GO:0006783, GO:0005506 | iD1, SPI1, Broad-complex_4, Broad-complex_3, ETS1, ELF5, Eip74EF, NHLH1, En1, NFYA, TBP, MEF2A, PEND, usp, Cebpa, ELK1, AGL3 |
| 6 | High in osteoblasts | Extracellular matrix | 220 | 138 | Ceecam1, Cilp, Col3a1, Col8a1, Col14a1, Ecm2, Eln, Fap, Fmod, Fndc1, Kera, Matn2, Matn4, Meox2, Mmp23, Spock3, Vcam1 | GO:0005578 | Klf4, MNB1A, PBF, id1, Dof3, MZF1_5-13, RUSH1-alfa, Gfi, Pax5, TFAP2A, TBP, IRF2, MEF2A, AGL3 |
| 10 | High in mature B cells > DC | B-cell activation/antigen presentation | 176 | 101 | Blr1, C2ta, Cd19, Cd22, Cd74, Cd79a, Cd79b, Fcer2a, H2-Oa, H2-Ob, Igh-1a, Lta, Ltb | GO:0042113, GO:0002504 | Eip74EF, SPIB, SPI1, Myf, IRF1, ETS1, STAT1, REL, RELA, TFAP2A, Dl_2, GABPA, Lhx3, NF-kappaB, ELK1, Mafb, MEF2A, Sox17, bZIP911, AGL3 |
| 14 | High in T cells > NK cells/DC | T-cell activation | 114 | 47 | Bcl11b, Cd3e, Cd3g, Cd28, Cd247, Itk, Lime1, Tcra, Tcrb-j, Tcrb-V13, Zap70 | GO:0042101, GO:0004872 | RREB1, Dof2, SPIB, SPI1, MNB1A, ETS1, ELF5, Staf, REL, Eip74EF, NHLH1, NF-kappaB, RELA, NFKB1 |
| 17 | High in endothelial cells | Endothelium-related | 91 | 62 | Esam1, Nos3, Pecam1, Sele, Selp | GO:0001525, GO:0007165, GO:0007154 | SPI1, ELF5, SPIB, Eip74EF, ETS1 |
| 18 | High in chondrocytes | Extracellular matrix | 86 | 53 | Agc1, Bmp5, Cart1, Chad, Col9a1, Col9a2, Col9a3, Fgfr3, Hapln1, Krt14, Loxl4, Matn1, Matn3, Omd | GO:0005578, GO:0044421, GO:0005615 | Myf, Dof2, PBF, MNB1A, TBP, AGL3, Evi1 |
| 23 | High in NK cells | NK-cell-related | 79 | 54 | Ctsw, Fasl, Gzma, Klra3, Klra5, Klra7, Klra12, Klra18, 20, Klra22, Notch2, Prf1 | Pax4, id1, MZF1_5-13, Broad-complex_1, SPIB, ELF5, ETS1, Eip74EF, RUNX1 | |
| 24 | High in mesenchymal cells/FDC | Mesenchyme-related | 75 | 46 | Acta2, Bgn, Col1a1, Col1a2, Col3a1, Col6a1, Col6a2, Fbn1, Il6st, Lox, Mmp2, Pcolce, Prrx1, Sgce, Twist1 | GO:0044420, GO:0005578, GO:0005581 | Klf4, hb, id1, HNF1A, MZF1_1-4, Broad-complex_4, SQUA, MNB1A, Dof2, PBF, SPI1, TBP, Staf, Dof3, FOXL1, Broad-complex_3, Cebpa, HMG-1, STAT1, Broad-complex_2, REL, AGL3, Athb-1, En1, MEF2A, SRY, RELA, Gfi, Agamous, dl_1, PEND, Sox5, ARR10, Nkx2-5, ABI4, HLF, SOX9, E2F1 |
| 25 | High in mesenchymal cells/FDC | Mesenchyme-related | 63 | 44 | Col5a2, Col12a1, Cthrc1, Edg2, Fzd1, Gpc6, Mgp, | GO:0005578, GO:0044421, GO:0005783 | NFYA, TEAD1, MYB.ph3, ABI4 |
| 28 | High in peritoneal macrophages > BMM/RAW264/microglia/osteoclasts | Phagocyte-related | 58 | 33 | Atg4c, Atp1a3, Atp6v0d2, Cdkn1c. Clec7a, Ctsb, Ctsl, Daglb, Edem2, Galc, Gpr175, Hipk2, Lgals3, Lhfpl2, Mamdc2, Matk, Naglu, Plekhm2, Rgl1, S100a1, Samd8,Snx27, Soat1, Spsb4, Tnfsf12, Tor2a, Tpcn2 | Pax4, Dof2, MNB1A, Staf, PBF, En1, ELK1, ovo, NFYA, RUNX1, MYB.ph3 | |
| 30 | High in myoblasts | Muscle-related | 56 | 38 | Chrna1, Des, Eno3, Kcnf1, Murc, Musk, Myf5, Myod1, | GO:0007517 | Myf, TBP, NHLH1, MEF2A, FOXL1, NFYA, AGL3, ABI4, GATA3 |
| 49 | High in macrophages/RAW264/microglia/osteoclasts | Phagocyte-related | 30 | 17 | Atp6v0c, Atp6v1a, Atp6v1b2, Atp6v1c1, Cln8, Ctsb, Gpnmb, Gusb, Htr2b, Lgmn, Tbc1d22a, Trem2 | GO:0015986 | No motifs identified |
Clusters generated from the cell-lineage expression data using BioLayoutExpress3D (see Supplementary material, Table S1; r=0·85, MLC = 2·2) were individually curated and annotated based upon examination of the average expression profile, GO terms and biological knowledge. Genes were chosen to represent known lineage or functional markers within each cluster. Statistically over-represented transcription factor binding sites within each cluster.
BMM, bone-marrow-derived macrophages; DC, classical dendritic cells; FDC, follicular dendritic cells; GO, gene ontology; NK, natural killer.
1
Over-represented transcription factors presented in order of over-representation.