TABLE 7.

Functional grouping of genes that are night/day differentially expressed (N/D >2 or <1/2) or at high levels (rEx >4) in the pineal gland

All genes appear in Tables 1 and 3 and, supplemental Tables S3 and S4.

Functional group	Gene symbol
Specialized processes
Immune response/inflammation	Abhd2,aAnd, Ahcy, Alms1,aArHgef9, Bbs7, Bcar1, Btg2, C3, Ccl2, Ccl6, Ccl7, Ccl9, Ccrl2,aCd1d1, Cd47, Cd74, Cd8a, Crcp, Ctsc, Ctss, Defb24, Dscr1, Fcer1a, Fras1,aGdf15, Gem,aHivep1, Hivep2, Icsbp1, Ifi35, IfiTm1,aIfnar1,aIgsf4a, Igsf9,aIgha, II13ra2, II17re, Il18, Il1rl1l, Ilk, Impdh2, Inhbb, Irak2, Irf7, Ler3, Litaf, Lrrc8, Lta4h, Mal2, Mdk, Mina, Mmd2, Mox2, Mx2, Oit1,aOptn, Pcna, Plscr1, Pvr, Pvrl2, RT1-A1, RT1-A2, RT1-A3, RT1-Aw2, RT1-Bb, RT1-Da, Sct2, Sema3a, Serping1, Slfn3, Stch, Stip1, Tfp12, Tpm4, Ush2a, Vof16
Melatonin synthesis	Aanat, Acly, Asmt, Ddc, Gch1, Gchfr, Mat2a, Pcbd1, Tph1
Photodetection	Genes linked to photodetection in the pineal gland are considered to be highly expressed in both the pineal gland and retina; they are listed in Table 4 and supplemental Table S5
T3/RA signaling	Dio2, Hr, Rbp3, Rdh12,aRorb,aRxrg, Thrb, Ttr
Nonspecialized processes
Adhesion	Cdh22, Celsr32, Cml5, Cntn4, Dsc2, Eva,aGja12,aGlycam1, Grn, Hnt, Mcam, Mfap4, Mpp4, Muc4, Nell2, Parvb, Pcdh21, Prph2, Pvr, Scarb2, Sdc4, Spon1, Ssx21p
Cell cycle/cell death	Acom1, Acvr1, Aprin, Bag1,aGiklk, Casp7, Ccnd2, Cdc25a, Cdc5l, Cdk5, Cdkn1b, Cdkn1c, Cflar, Ches1,aCommd5, Csnk2a2, Ddit3, Dnm1, Dnm2, Elmo3, Faim, Gos2, Gadd45a, Gadd45b, Igf1r, Igfbpl1,aJag1, Junb, Mad2l2, Mak10, Ntf3, Pafah1b1, Pard3, Pdia3, Plagl1, Ptgs2, Qscn6, Rarres1, Rgc32, Fhob, Slc31a1, Strn3, Tacc3, Vegfc
Cytoskeleton	Ap1g1, Baiapw, Bbs4,aCatna1, Clasp2, Clta, Col14a1,aCol3a1, Col4a3, Col8a1,aCope,aCpg2, Dnch1, Dncl2b,aDncl2b,aEmilin1,aEmls, Fgd2,alnb,aFlnc,aFmod, Fni, Fscn2,aHdac11,aKa15, Kif1b, Kif22, Kif2c, Krt1-18, Krt1-19, Krt25, Lad1,aLama2,aLamb1-1,aLap1b, Lcp1, Lix1, Lmod1, Lumk, Mapt, Marcks, Mfap5,aMgp, Mrgl19, Mtap2, Mylip,aNrap,aPgea1, Rpl3, Sas, Selpl,aSdo3, Spna2, Tctex1, Thbs4, Tmem16a,aTmem22, Tpm4, Tuba4, Tubb5, Unc119, Vil2, Vim
DNA modification	Adprt, Blm,aBnc2,aCntn1, Commd1,aCtps,aHerc3,aHmgb2, Kpna2, Mcm4, Pcna, Prc1,aPrim1, Ptms, Rere, Thap4, Tlk1,aTop1, Tspyl4, Zdhhc22, Zfp143, Zfp162, Zfp238, Zfp36l1, Zhx1, Znf444, Zswim5,a
Endothelium	Esm1, Vegfb, Vegfc, Vwf
Growth	Efemt1, Egf, Egfr, Egfr1, Fgf1, Fgfr1, Gadd45g, Gdf15, Gfer, Grb2, Igf1r, Igfbp2, Igfbp6, Pdgfrl, Pgf, Tgfb1, Tgfbi, Vegfb, Vegfc
Signaling	Calcium: Atp2b3, Cabp1, Cacna1f, Cacna1g, Calm1, Camk1g, Camk2b, Cip98, Dcamkl1, Dcamkl3
	Cyclic nucleotide: Adcy8, Akap11, Cnga1, Cngb1, Creb3, Guca1a, Gucy1a3, Hcn1, Pde4b, Pde4d, Pde6b, Pde8b, Pde10a, Prkar2b, Prkca
	G-protein: Arf3, Arr3, Arl2bp, Arl6ip5, Gem, Gna12, Gnaq, Gnas, Gnat2, Gnaz, Gnb1, Gnb3, Gng11, Grk1, Pdc1, Rgs2, Rgs4, Rgs7, Rgs9, Rgs17, Sag1, Tyro3
	Membrane receptors/ligands: Acvr1, Adra1b, Adrb1, Agtrap, Bmp6, Chrna3, Chrnb1, Chrnb4, Crcp, Drd1a, Drd4, Ece1, Ednrb, Egf, Egfr, Fgf, Fgfr1, Fst, Fzd4, Grip2, Grm1, Grm2, Hcrtr1, Htr2c, Igf1r ,Igfbp2, Igfbp3, Igfbp5, Igfbp6, Lepr, Nog, Opn1sw, Prlr, Sort1, Vipr2
	Lipid/ Phospholipid/cholesterol: Abca1,Alox15, Cyp27a1, Ephx1, Inpp5e, Itpr1, Lta4h, Ltb4dh, Pa2g1b, Pik3r3, Pla2g5, Plcb1, Plcd4, Ptgds, Ptgis
	MAP kinase: Dusp1, Errfi1, Map3k5, Map3k6, Map4k1, Mapk14, Mapk6
	Protein phosphorylation, serine/threonine: Calm1, Camk1g, Camk2b, Cdk5, Cdkn1b, Crkas, Dcamkl1, Enh, Fez1, Gsk3b, Nell2, Pak2, Prkar2b, Prkca, Prkcdbp, Prkce, Prkcl1, Rock2, Sik2, Snrk, Stk2, Stk39
	Protein phosphorylation, tyrosine: Crkas, Efna5, Jak1, Kit, Ntrk2, Ntrk3, Ptp2E, Ptp4a1, Ptpn16, Ptprj, Ptprr, Ptp-Td14, Tyro3
RNA modification	Ankrd24,aBfsp1, Bop1, Bzw2, Eif2ak4,aEif2c2, Eif3s9, Eif4g2, Ell2, Hdac5, Polr2d,aQtrt1, Rnase1, Rnase2,aRpat1, Sfpq, Xpota
Small molecule biology	Metal homeostasis: Atp7b, Chordc1, Mt1a, Mt2, Slc30a1 Slc39a4
	Ion homeostasis: Atp1a1, Atp1b1, Atp1b2, Atp2a2, Atp2b1, Cacna1h, Cacnb2, Clcn3, Cnga1, Cngb1, Hcn1, Kcnab2, Kcne2, Kcnh6, Kcnj14, Kctd3, Scn7a, Slc12a2, Slc12a5, Slc17a6, Slc24a1
	Solute transport: Slc2a1, Slc2a4, Slc3a1, Slc4a2, Slc4a4, Slc6a6, Slc7a1, Slc7a7, Slc12a2, Slc12a5, Slc14a1, Slc15a1, Slc16a1, Slc16a6, Slc21a1, Slc21a7, Slc22a1, Slc25a10, Slc29a1, Slc30a1, Slc34a1
Transcription factors	Arntl, Bhlhb3, Cebpb, Crem, Cbx5, Cry2, Crx, Datf1, Eya2, Fosl2, Foxd1, Hdac5, Homer1, Homer2, Hr, Isl2, Jun, Junb, Mitf, Msx1, Neurod1, Nr1d2, Nr1h4, Nr2f6, Nr4a1, Nr4a3, Otx2, Pax4, Pax6, Per2, Ptch1, Rax, Rorb, Rxrg, Thrb
Vesicle biology	Cadps, Chga, Chgb, Clta, Cltb, Dnm1, Dnm2, Dnm3, Lphn2, Ptprn, Scg2, Scg3, Snap23, Snap25, Sny2, Stx3, Sv2b, Syt4

^aPredicted gene is indicated.