Table S1 The four gene sets derived from gene expression profiles of ESCs and differentiated cells Uniform High Uniform Low ES Up ES Down EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol 269261 Rpl12 11354 Abpa 68239 Krt42 15132 Hbb-bh1 67891 Rpl4 11537 Cfd 26380 Esrrb 15126 Hba-x 55949 Eef1b2 11698 Ambn 73703 Dppa2 15111 Hand2 18148 Npm1 11730 Ang3 67374 Jam2 65255 Asb4 67427 Rps20 11731 Ang2 22702 Zfp42 17292 Mesp1 15481 Hspa8 11807 Apoa2 58865 Tdh 19737 Rgs5 100041686 LOC100041686 11814 Apoc3 26388 Ifi202b 225518 Prdm6 11983 Atpif1 11945 Atp4b 11614 Nr0b1 20378 Frzb 19241 Tmsb4x 12007 Azgp1 76815 Calcoco2 12767 Cxcr4 20116 Rps8 12044 Bcl2a1a 219132 D14Ertd668e 103889 Hoxb2 20103 Rps5 12047 Bcl2a1d 381411 Gm1967 17701 Msx1 14694 Gnb2l1 12049 Bcl2l10 20899 Stra8 23796 Aplnr 19941 Rpl26 12096 Bglap1 78625 1700061G19Rik 12627 Cfc1 12070 Ngfrap1 12097 Bglap2 21816 Tgm1 12622 Cer1 19989 Rpl7 12267 C3ar1 67405 Nts 21385 Tbx2 19896 Rpl10a 12279 C9 435337 EG435337 56720 Tdo2 20044 Rps14 12391 Cav3 545913 Zscan4d 16869 Lhx1 19175 Psmb6 12409 Cbr2 244448 Triml1 22253 Unc5c 22627 Ywhae 12477 Ctla4 69134 2200001I15Rik 14174 Fgf3 19951 Rpl32 12523 Cd84 66065 Hsd17b14 16542 Kdr 66152 1110020P15Rik 12524 Cd86 81879 Tcfcp2l1 15122 Hba-a1 66489 Rpl35 12640 Cga 17907 Mylpf 15414 Hoxb6 15519 Hsp90aa1 12642 Ch25h 26424 Nr5a2 210530 Leprel1 66483 Rpl36al 12655 Chi3l3 83560 Tex14 12338 Capn6 27370 Rps26 12796 Camp 17450 Morc1 20671 Sox17 66576 Uqcrh 12869 Cox8b 79455 Pdcl2 20613 Snai1 22154 Tubb5 12959 Cryba4 231821 Centa1 17897 Myl3 15516 Hsp90ab1 12981 Csf2 67968 Ooep 22139 Ttr 20055 Rps16 12993 Csn1s2a 258369 Olfr509 15410 Hoxb3 18746 Pkm2 13011 Cst7 76572 Rbmxl2 14465 Gata6 76846 Rps9 13035 Ctsg 12745 Clgn 15407 Hoxb1 276770 Eif5a 13086 Cyp2a4 12808 Cobl 268288 Samd3 13629 Eef2 13094 Cyp2b9 11670 Aldh3a1 18417 Cldn11 11947 Atp5b 13096 Cyp2c37 21432 Tcl1 58188 Vstm2b 11461 Actb 13098 Cyp2c39 14562 Gdf3 19142 Prss12 15254 Hint1 13099 Cyp2c40 14275 Folr1 15376 Foxa2 19716 Bex1 13108 Cyp2g1 20750 Spp1 58802 Kcnmb4 22003 Tpm1 13112 Cyp3a11 13590 Lefty1 15227 Foxf1a 12317 Calr 13184 Dcpp1 59290 Gpa33 22413 Wnt2 27050 Rps3 13215 Defb2 18778 Pla2g1b 15135 Hbb-y 11674 Aldoa 13237 Defcr3 216166 6330514A18Rik 14170 Fgf15 67678 Lsm3 13239 Defcr5 73914 Irak3 14463 Gata4 73830 Eif3k 13525 Adam26a 12051 Bcl3 21952 Tnni1 12785 Cnbp 13586 Ear1 27052 Aoah 14028 Evx1 19934 Rpl22 13587 Ear2 258430 Olfr938 236920 Stard8 20194 S100a10 13615 Edn2 56312 Nupr1 666794 Rbm24 23837 Cfdp1 13856 Epo 12389 Cav1 11694 Alx3 13627 Eef1a1 14029 Evx2 546024 Crxos1 12160 Bmp5 19240 Tmsb10 14038 Expi 328381 Sh2d4b 216725 Adamts2 13681 Eif4a1 14080 Fabp1 13417 Dnahc8 13380 Dkk1 170676 Peg10 14089 Fap 14711 Gnmt 494504 Apcdd1 26961 Rpl8 14127 Fcer1g 74400 Zfp819 23831 Car14 12466 Cct6a 14133 Fcna 50796 Dmrt1 67389 C1qdc2 68735 Mrps18c 14134 Fcnb 381142 Gm949 56096 Plac1 22166 Txn1 14180 Fgf9 13730 Emp1 258627 Olfr1504 20042 Rps12 14308 Fshb 14120 Fbp2 18186 Nrp1 12465 Cct5 14377 G6pc 66957 Serpinb11 21924 Tnnc1 16852 Lgals1 14405 Gabrg1 240095 H2-M5 278240 Spin2 22381 Wbp5 14406 Gabrg2 434203 Slc28a1 14165 Fgf10 67186 Rplp2 14429 Galr3 16952 Anxa1 22418 Wnt5a 67130 Ndufa6 14525 Gcet2 268491 Gm1564 14586 Gfra2 20422 Shfm1 14539 Opn1mw 20210 Saa3 18760 Prkd1 67267 2900010M23Rik 14599 Gh 22041 Trf 18606 Enpp2 228033 Atp5g3 14603 Gif 385343 Rhox1 20730 Spink3 20084 Rps18 14610 Gja10 67664 Rnf125 69553 2310033K02Rik 22070 Tpt1 14625 Gykl1 245109 Gm397 380686 Cnrip1 71679 Atp5h 14714 Gnrh1 14175 Fgf4 12778 Cxcr7 26443 Psma6 14715 Gnrhr 67981 Hormad1 209195 Clic6 68045 2700060E02Rik 14727 Gp49a 94244 Fkbp6 503491 Defcr24 192170 Eif4a3 14738 Gpr12 214133 Tet2 57246 Tbx20 66414 Ndufa12 14857 Gsta1 16600 Klf4 14934 Gypa 15384 Hnrnpab 14945 Gzmk 269637 Cnpy1 20583 Snai2 16691 Krt8 15061 H28 66991 2410004A20Rik 54613 St3gal6 67941 Rps27l 15171 Hcrt 93672 Il24 14460 Gata1 11465 Actg1 15202 Hemt1 11815 Apod 67580 Lrrc18 17242 Mdk 15234 Hgf 11828 Aqp3 73230 Bmper 16828 Ldha 15402 Hoxa5 71981 Tdrd12 14176 Fgf5 15191 Hdgf 15403 Hoxa6 56643 Slc15a1 240168 Rasgrp3 12464 Cct4 15458 Hpx 58206 Zbtb32 27494 Amot 68193 Rpl24 15465 Hrh1 207839 Galnt6 214968 Sema6d 72931 2900010J23Rik 15486 Hsd17b2 15162 Hck 75480 1700003F12Rik 19385 Ranbp1 15495 Hsd3b4 434423 Dppa5a 230587 Glis1 319169 Hist1h2ak 15496 Hsd3b5 18173 Slc11a1 16842 Lef1 56347 Eif3c 15874 Iapp 434769 Rhox10 320508 Cachd1 14228 Fkbp4 15962 Ifna1 20618 Sncg 19051 Gsbs 67160 Eef1g 15964 Ifna11 50764 Fbxo15 269831 Tspan12 53356 Eif3g 15968 Ifna5 66222 Serpinb1a 66104 Tceal6 12856 Cox17 15970 Ifna7 74434 Sohlh2 78473 Skap1 18477 Prdx1 15974 Ifnab 16598 Klf2 14587 Gfra3 56040 Rplp1 15977 Ifnb1 54427 Dnmt3l 16552 Kif12 19185 Psmd4 16153 Il10 54204 1-Sep 15484 Hsd11b2 53379 Hnrnpa2b1 16158 Il11ra2 208080 Gm514 15429 Hoxd1 20823 Ssb 16159 Il12a 75828 Hormad2 76441 Daam2 12626 Cetn3 16171 Il17a 21689 Tekt1 21349 Tal1 97122 Hist2h4 16181 Il1rn 195349 Btnl7 15214 Hey2 18643 Pfn1 16333 Ins1 109820 Pgc 18546 Pcp4 19052 Ppp2ca 16334 Ins2 22788 Zp3 18205 Ntf3 26441 Psma4 16415 Itgb2l 242509 Bnc2 27217 Mixl1 18107 Nmt1 16616 Klk1b21 16421 Itgb7 101772 Tmem16a 15081 H3f3b 16619 Klk1b27 231125 Zfyve28 20682 Sox9 67788 6330577E15Rik 16622 Klk1b5 14130 Fcgr2b 16826 Ldb2 18655 Pgk1 16624 Klk1b8 239188 Enox1 76157 Slc35d3 69126 1810022K09Rik 16628 Klra10 20306 Ccl7 245595 Zfp711 109672 Cyb5 16630 Klra12 246177 Myo1g 70392 Asb12 12461 Cct2 16631 Klra13 228550 Itpka 20680 Sox7 66684 Tceal8 16635 Klra4 19725 Rfx2 22359 Vldlr 13205 Ddx3x 16636 Klra5 320435 5830482F20Rik 20472 Six2 22142 Tuba1a 16638 Klra7 230073 Ddx58 11687 Alox15 17999 Nedd4 16639 Klra8 23886 Gdf15 54216 Pcdh7 12868 Cox8a 16640 Klra9 75600 Calml4 83691 Crispld1 20867 Stip1 16642 Klrc2 74249 Lrrc2 19731 Rgl1 14109 Fau 16643 Klrd1 16331 Inpp5d 329872 Frem1 66870 Serbp1 16699 Krtap13 19225 Ptgs2 12562 Cdh5 68598 Dnajc8 16701 Krtap6-2 232431 Gprc5a 239743 Klhl6 110323 Cox6b1 16704 Krtap8-2 243911 Kirrel2 21389 Tbx6 11739 Slc25a4 16705 Krtap9-1 22422 Wnt7b 70127 Dpf3 66131 Tipin 16963 Xcl1 17916 Myo1f 22065 Trpc3 66537 Pomp 17059 Klrb1c 72685 Dnajc6 78465 1700084C01Rik 17748 Mt1 17084 Ly86 69540 Klk10 12561 Cdh4 16668 Krt18 17137 Magea1 18682 Phkg1 12918 Crh 12469 Cct8 17138 Magea2 63872 Zfp296 15001 H2-Oa 19045 Ppp1ca 17139 Magea3 20728 Spic 16728 L1cam 67281 Rpl37 17141 Magea5 12894 Cpt1a 242259 Slc44a5 55989 Nol5 17142 Magea6 18787 Serpine1 67182 Pdzk1ip1 12215 Bsg 17144 Magea8 378435 Mafa 65963 Tmem176b 14775 Gpx1 17145 Mageb1 237930 Ttll6 66607 Ms4a4d 13014 Cstb 17146 Mageb2 110173 Manba 67742 Samsn1 30795 Fkbp3 17230 Tpsab1 20493 Slc10a1 76933 Ifi27 245688 Rbbp7 17251 Mds1 73032 Ttc9b 67252 Cap2 18648 Pgam1 17700 Mstn 12308 Calb2 15110 Hand1 20068 Rps17 17773 Mtnr1a 18049 Ngf 215303 Camk1g 19170 Psmb1 17830 Muc10 433719 OTTMUSG00000001246627191 Tmem90a 68953 Chmp2a 17840 Mup1 216445 Arhgap9 14184 Fgfr3 19179 Psmc1 17841 Mup2 17752 Mt4 15203 Heph 69833 Polr2f 17843 Mup4 237360 Adamts14 16392 Isl1 19983 Rpl5 17844 Mup5 83558 Tex11 432677 7420416P09Rik 12462 Cct3 17877 Myf5 73660 Cabp4 14247 Fli1 11958 Atp5k 17940 Naip1 109904 Mcf2 20686 Spa17 11816 Apoe 18048 Klk1b4 77485 Stk31 12351 Car4 57423 Atp5j2 18050 Klk1b3 57746 Piwil2 13143 Dapk2 68202 Ndufa5 18092 Nkx2-6 68236 Gtsf1l 19885 Rorc 70186 2310056P07Rik 18168 Npy5r 100043100 Rp23-282c23.3 54409 Ramp2 20527 Slc2a3 18261 Ocm 13614 Edn1 72630 Hspa12b 20054 Rps15 18285 Odf1 54169 Myst4 13082 Cyp26a1 19167 Psma3 18307 Olfr10 20389 Sftpc 66058 Tmem176a 170791 Rbm39 18310 Olfr13 14348 Fut9 72865 Cxx1c 12864 Cox6c 18314 Olfr17 83961 Nrg4 14451 Gas1 14678 Gnai2 18315 Olfr18 105450 Mmrn2 211134 Lzts1 18103 Nme2 18316 Olfr19 226652 Arhgap30 17150 Mfap2 54124 Cks1b 18317 Olfr2 14164 Fgf1 21350 Tal2 14860 Gsta4 18323 Olfr25 12064 Bdnf 21387 Tbx4 21371 Tbca 18328 Olfr3 94092 Trim16 54562 Lrrc6 18458 Pabpc1 18329 Olfr30 69824 Glod5 64074 Smoc2 69639 Exosc8 18330 Olfr31 14942 Gzme 19228 Pthr1 70356 St13 18332 Olfr33 52670 Cpsf4l 68910 Zfp467 75316 Josd3 18341 Olfr42 170734 Zfp371 16373 Irx3 406217 Bex4 18343 Olfr44 241230 St8sia6 20356 Sema5a 68836 Mrpl52 18346 Olfr47 67689 Aldh3b1 170722 Nxf7 54709 Eif3i 18347 Olfr48 381371 Gm1631 71693 Colec11 114641 Rpl31 18349 Olfr5 626316 OTTMUSG0000001017314462 Gata3 59013 Hnrnph1 18352 Olfr52 12994 Csn3 20708 Serpinb6b 13690 Eif4g2 18354 Olfr54 77632 Pramef12 15117 Has2 76808 Rpl18a 18357 Olfr57 16667 Krt17 72780 Rspo3 50783 Lsm4 18358 Olfr58 22361 Vnn1 66748 4933404M02Rik 67106 Zbtb8os 18362 Olfr61 14618 Gjb1 18530 Pcdh8 56495 Asna1 18367 Olfr66 71733 Susd2 272381 Lrrc4b 17184 Matr3 18368 Olfr67 74186 Ccdc3 16592 Fabp5 58810 Akr1a4 18370 Olfr69 83563 Usp26 53416 Stk39 66212 Sec61b 18372 Olfr8 108075 Ltbp4 16909 Lmo2 22352 Vim 18422 Ott 17182 Matn3 77794 Adamtsl2 66413 Psmd6 18489 Reg3b 13067 Cyct 16371 Irx1 22121 Rpl13a 18722 Pira1 381308 Mnda 11517 Adcyap1r1 16211 Kpnb1 18725 Pira2 69863 1810054D07Rik 27205 Podxl 270106 Rpl13 18776 Prl3b1 629756 Wfdc10 106648 Cyp4f15 225896 D19Ertd721e 18811 Prl2c2 70274 Ly6g6e 17130 Smad6 16783 Lamp1 18812 Prl2c3 57875 Angptl4 15416 Hoxb8 66070 Cwc15 18814 Prl7d1 252830 Obox6 17702 Msx2 16412 Itgb1 18828 Plscr2 347711 Pramel6 54195 Gucy1b3 66916 Ndufb7 18829 Ccl21b 98558 Mael 18018 Nfatc1 107435 Hat1 18843 Plunc 67656 4930548H24Rik 14179 Fgf8 66384 Srp19 18998 Pou4f3 235628 Tessp2 14619 Gjb2 66181 Nola3 19064 Ppy 243874 Nlrp9b 72690 Grrp1 21402 Skp1a 19109 Prl 243659 Styk1 17174 Masp1 18538 Pcna 19114 Prl7a2 20868 Stk10 72668 2810030E01Rik 19166 Psma2 19118 Prm1 328795 Ubash3a 16521 Kcnj5 21991 Tpi1 19119 Prm2 76797 2410137M14Rik 77701 Lcn12 19988 Rpl6