Table 2 of Geisert, Mol Vis 2009; 15:1730-1763.

Table 2. Signature genes for cells, tissues, and systems of the mouse eye

Index Cell, tissue, or system Primary gene signatures Probe set IDs Secondary signatures
1 Sclera, firoblast cells Aebp1, Bgn, Fmod, Mxra8, Pcolce 1422514_at, 1416405_at, 1415939_at, 1452330_a_at, 1448433_a_at Aldh2, Bgn, Col6a2, Enpp3 Igfbp6, Krt13, Lgals3, Mmp1, Mmp2, Mmp3, Scel, Serpinf1, Serping1, Sfn, Slc6a14, Timp1, Timp2, Timp3
2 Sclera and cornea, fibroblasts (generic) Col1a1, Col1a2, Sparc 1423669_at, 1450857_a_at, 1448392_at
3 Cornea, epithelial cells, squamous cells Aldh3a1, Dsp, Krt12, Pkp1, Tjp3 1418752_at, 1435494_s_at, 1419230_at, 1449586_at, 1417896_at Aqp3, Aqp5, Col5a2, Col6a3, Col12a1, Col17a1, Cs1, Dsg1, Dsc3, Gja1, Klf4, Klf5, Krt3, Krt17, Lgals3, Lypd3, Pax6, Perp, Tacstd2, Tkt, Upk1b
4 Cornea, epithelium, basal cells (cuboidal, Bowman's layer associated) Col17a1, Sdc1, Tgfbi 1418799_a_at, 1415944_at, 1415871_at Col7a1, Gsta4, Itga6, Ptgr1, Trp63
5 Cornea and conjunctiva, limbal stem cells (and basal cells) Kit, Mki67, Trp63 1452514_a_at, 1426817_at, 1418158_at Abcg2, Ereg, Nes, Pax6
6 Cornea, stromal fibroblast keratocytes (neural crest derived) Col1a1, Col5a1, Col6a1, Col6a3, Kera, Lum 1423669_at, 1416740_at, 1448590_at, 1424131_at, 1418063_at, 1423607_at Abcg2, Aim1, Aldo3, Aqp1, Col5a2, Cyp4v2, Dcn, Evpl, Fmod, Gsn, Gsta4, Gsto1, Krt5, Ogn, Ppl, Ptgds, Sfn, Sgce, Tacstd2, Tkt, Vim
7 Cornea, endothelial cells (neural crest derived, Descemet's membrane associated) Col3a1, Mmp14, Slc4a11, Tgfbi, Wasf2 1427883_a_at, 1448383_at, 1434867_at, 1448123_s_at, 1454673_at Aqp1, Apod, Car12, Cd274,Cd276, Col8a1, Col8a2, Dcn, Krt5, Krt12, Pitx2, Ptgs2, Svep1
8 Conjunctiva, epithelium, squamous cells Krt7, Krt8 1423952_a_at, 1423691_x_at Krt13, Krt14, Krt19
9 Conjunctiva, goblet cells Muc5ac 1430899_at Muc1, Muc4
10 Anterior segment, leukocytes, macrophages, microglia Cd68, Ifitm1, Ly6a, Ly6e, Ptprc 1449164_at, 1424254_at, 1417185_at, 1453304_s_at, 1422124_a_at Cd53, Hexb, Itgam, Lcp1, Lyve1, Tyrobp
11 Anterior segment, dendritic cells Ctsc, Tlr2, Tlr3 1416382_at, 1419132_at, 1422782_s_at Bcl10, Ctsc, Ifih1, Ifi202b, Tmem176b/Lr8, Il2rb
12 Anterior segment, T regulatory cells Il2ra, Foxp3 1420692_at, 1420765_a_at Cd4, Ctla4, Il2rb
13 Anterior segment, cytotoxic T cells Cd8a, Ctsw, Gzbm 1440164_x_at, 1422632_at, 1419060_at Cd28, Ctsw, Fasl, Prf1
14 Anterior segment, NK natural killer cells Cd7, Klrb1c, Klrg1 1419711_at, 1449570_at, 1420788_at Ctsw, Fcgr3, Klra17, Klrb1c, Klrd1, Klrk1, Ncam
15 Anterior segment, immune suppression Cd55, Cd274 1418762_at, 1419714_at Cd46, Cd59, Cd276, C3ib, Cgrp, Il1ra, Pomc1, Sst, Tgfb2, Tsp1, Vip
16 Anterior segment, classical complement pathway C1qg, C1r, C1s, Ctss 1449401_at, 1417009_at, 1424041_s_at, 1448591_at Bf, C1qa, C1qb, C2, C4b, Cd59, Ccl3, Ccl4, Cd14,Cd68, Coro1a, Csf1r, Ctss, Daf, Fcgf2b, Fcgr3, Serping1, Tyrobp
17 Lymphatic endothelial cells Lyve1, Pdpn, Prox1 1429379_at, 1419309_at, 1421336_at Flt4, Vegfc, Figf
18 Extraocular muscles Atp2a1, Mylpf, Tnnc2, Tnni2, Tpm1 1419312_at, 1448371_at, 1417464_at, 1416889_at, 1423049_a_at Acat1, Ache, Actc1, Actn3, Bgn, Cacng1, Chrna1, Ckm, Eno3, Lmod1, Mybpc2, Myh1, Myh4, Myh13, Pitx2, S100a1, Slc4a3, St8sia4, Tnni1, Tnnt2, Tnnt3, Tnt2, Tpm2, Ttn, Wsf1
19 Aterrioles, smooth muscles Cnn2, Myl9, Tgln, 1450981_at, 1452670_at, 1423505_at Acta2, Cnn2, Flna, Kcna3, Lmo2, Hdac9, Tpm2
20 Arterioles, endothelial cells Efnb2, Efna1 1419639_at, 1416895_at Adra2a, Kcna2, Nos3, Pecam1
21 Vasculature, capillaries, endothelial cells Edg3, Pecam1, Vcam1 1438658_a_at, 1421287_a_at, 1448162_at Ace, Ccl7, Ccl2, Ccl8, Cd31, Cd34, Cd105. Cd144, Cd248, Cd146, Cdh5, Cxcl1, Cxcl2, Cxcl3, Cxcl6, Edn1, Glycam1, Klf6 Nos3, Icam1, Il6, Ptprm, Plxdc1, Sele, Thbd, Vezf1
22 Vasculature, venules, endothelial cells Nr2f2 1416158_at Klf6
23 Lens, capsule, equitorial region, epithelial cells Cryga, Crygf, Hspb1, Lenep 1422652_at, 1429948_x_at, 1425964_x_at, 1422309_a_at Ablim, Cav1, Cltcl1, Cryba1, Crybb2, Crybb3, Crygb, Crydg, Crygs, Epb41l1, Epb49, Foxe3, Gsr, Gss, Maf, Picalm, Psip1, Prma7, Psma6, Psmb6, Psmb7, Psmb9, Psmd13, Sod1, Sorbs1, Sox1, Sptbn2, Tcp11
24 Lens, fiber cells (primary, secondary), core and cortex Bfsp1, Bfsp2, Mip 1450571_a_at, 1434463_at, 1421039_at Birc7, Lim2, Pacsin3
25 Intrinsic eye muscles, sphincter and dilator Casq2, Mybpc1, Tnni1 1422529_s_at, 1455645_at, 1450813_a_at Actg2, Ckmt2, Flnc Ppp1r12b, Myh2, Myh7, Tnni1, Tns1, Tpm3
26 Melanocytes (general) Mlph, Myo5a, Rab27a 1449896_at, 1419754_at, 1425285_a_at Edn3, Mltf, Notch2, Pldn
27 Iris stromal pigment cells, iris pigment epithelium, myoepithelium Oca2, Slc45a2, Tyr 1418211_at, 1451055_at, 1417717_a_at Clu, Mlph, Si
28 Ciliary process Dct, Mlana, Tyrp1 1418028_at, 1430635_at, 1415862_at Acta2, Adra2a, Arid5b, Gsta3, Hnmt, Hoxa10, Hoxa11, Krt8, Krt18, Mgll, Mlph, Pbx1, Si, Slc45a2, Srf
29 Hyalocytes of the vitreous humor Has2, Has3 1418678_at, 1420589_at Cd44, Cmas
30 Trabecular meshwork, trabeculocytes A2m, Gsn, Mxra8, Myoc 1434719_at, 1415812_at, 1452330_a_at, 1450468_at, Angptl7, Apod, Bgn, Ctgf, Foxc2, Gpnmb, Lgals8, Myoc, Pcolce, Scgb1a1, Sdc4, Sepp1, Serping1, Thbs1, Thbs2, Tnmd, Vim
31 Choroid, choriocapillaris, choroidal endothelial cells Ptgds 1449164_at
32 Retina, retinal pigment epithelium Rpe65, Rdh5, Rgr Rrh, Ttr 1418808_at, 1422832_at, 1450197_at, 1450280_a_at, 1459737_s_at Appbp1, Best1, Cst3, Ctsd, Kcnj13, Krt8, Krt18, Lrat, Mct3, Mct3l, Ptpgs, Rbp1, Slc16a8, Trf, Vmd2,
33 Retina, Müller glial cells Slc1a3 1443749_x_at Gfap, Glul, Rdh10, Slc6a1, Slc1a3, Vim
34 Retina, rod photoreceptors Rho 1425172_at Abca4, Cnga1, Gngt1, Sag, Pdc, Pde6g, Pde6b, Rom1
35 Retina, cone photoreceptors, M type (green) Opn1mw 1419723_at Arr3, Gnat2, Guca1a
36 Retina, cones, UV/S type (blue) Opn1sw 1449132_at Nr2e3, Thrb (developmental)
37 Retina, horizontal cells Calb1 1417504_at Lhx1, Prox1, Stx4a, Sept4,
38 Retina, bipolar cells (generic) Vsx2 1419628_at Bhlhb4, Cabp5, Gabrr2, Gnao1, Gng13, Hcn3, isl1
39 Retina, OFF cone bipolar cells Tacr3, Vsx1, Glrb 1437029_at, 1450487_at, 1422504_at Atp2b1, Gria2, Kcnip3, Neto1
40 Retina, ON cone bipolar cells Gja7 1447787_x_at
41 Retina, rod bipolar cells Grm2 1435607_at Glrb, Pcp2, Prkca
42 Retina, amacrine cells, glycinergic Slc6a9 1431812_a_at Cd44
43 Retina, amacrine cells, AII rod type Dab1, Gria3 1435578_s_at, 1438752_at Dab1, Gja9, Glra3, Ppp1r1b, Stx1a
44 Retina, amacrine cells, A17 type (serotonin-accumulating, reciprocal) Slc6a4 1417150_at Pah
45 Retina, amacrine cells, A18 dopaminergic Th 1420546_at
46 Retina, amacrine cells, GABA-ergic Gad1, Gad2 1416561_at, 1429589_at Cd15, Grid1, Grid2, Per1, Slc6a4
47 Retina, amacrine cells, cholinergic starburst Chat 1446681_at Kcnc1, Kcnc2
48 Retina, retinal ganglion cells, generic Chrna6, Nrn1, Gap43, Thy1 1450427_at, 1428393_at, 1423537_at, 1423135_at Bex1, Bex2, Calb2, Cerkl, Cplx1,Gja7, Map1a, Nef1, Nfl, Opn4, Pou4f1, Pou4f2, Pou4f3, Resp18, Stmn2, Slc17a6, Sncg, Vamp1, Vsnl1, Ywhah
49 Retina, retinal ganglion cells, melanopsin photosensitive Opn4 1421584_at
50 Retina and optic nerve, astrocytes Gfap 1426508_at Slc6a1, Vim, Slc1a3, Stat3
51 Optic nerve, Oligodendrocytes Mog 1448768_at Cldn11, Mag, Mbp, Mobp, Olig1, Plp1, Ugt8a
52 Immediate-early response Egr1, Fos 1417065_at, 1423100_at Jun, Ier2, Ier5
53 Transcription Creb1, Rbbp6 1428755_at, 1426487_a_at
54 Histone modification Hdac2, Mbd1, Sirt1 1445684_s_at, 1430837_a_at, 1418640_at Hdac3, Hdac7a, Hinfp, Mecp2, Rbbp7
55 Cell cycle Cdc2a, Cdc20, Mki67 1448314_at, 1439377_x_at, 1426817_at Birc5, Ccnb1, Cks2, Top2a
56 Circadian rhythm Arntl, Clock, Per1, Per2 1425099_a_at, 1418659_at, 1449851_at, 1417603_at Cry2, Dbp, Npas2
57 miRNA processing Dicer1, Mtf1, Rnasen 1460571_at, 1428979_at 1428656_at Pasha
58 Apoptosis, unfolded protein response Apaf1, Cap12 1452870_at, 1449297_at
59 Anti-viral interferon induced response Ifit1, Oas1g, Oas2 1450783_at, 1424775_at, 1425065_at Ifi1, Irf7, Mx1
60 Oxidative phosphorylation, mitochondrial complex I, III, IV Cox8a, Ndufa11, Ucrc 1448222_x_at, 1429708_at 1424364_a_at Nd5, Ndufb2, Ndufb10, Ndufs8,

We have compiled a list of some of these signatures and present them in Table 2. As an example we can look at the cornea signature which uses Aldh3a1 a corneal crystallin as a primary genetic tag and we can identify secondary signature genes.

Geisert, Mol Vis 2009; 15:1730-1763. http://www.molvis.org/molvis/v15/a185

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