Supp Table 12, Dichaete core bound Drosophila orthologues of mouse Sox2 bound genes ID Gene Symbol FBgn0000071 Amalgam Ama FBgn0000163 bazooka baz FBgn0000179 bifid bi FBgn0000233 buttonhead btd FBgn0000242 Beadex Bx FBgn0000253 Calmodulin Cam FBgn0000273 cAMP-dependent protein kinase 1 Pka-C1 FBgn0000287 spalt-related salr FBgn0000395 crossveinless 2 cv-2 FBgn0000411 Dichaete D FBgn0000413 daughterless da FBgn0000414 Disabled Dab FBgn0000448 Hormone receptor-like in 46 Hr46 FBgn0000459 disconnected disco FBgn0000463 Delta Dl FBgn0000464 Leukocyte-antigen-related-like Lar FBgn0000492 Drop Dr FBgn0000524 deltex dx FBgn0000535 ether a go-go eag FBgn0000546 Ecdysone receptor EcR FBgn0000568 Ecdysone-induced protein 75B Eip75B FBgn0000575 extra macrochaetae emc FBgn0000591 Enhancer of split m8, helix-loop-helix E(spl)m8-HLH FBgn0000625 eyegone eyg FBgn0000635 Fasciclin 2 Fas2 FBgn0000659 fork head fkh FBgn0001085 frizzled fz FBgn0001090 bangles and beads bnb FBgn0001139 groucho gro FBgn0001145 Glutamine synthetase 2 Gs2 FBgn0001147 gooseberry-neuro gsb-n FBgn0001148 gooseberry gsb FBgn0001168 hairy h FBgn0001170 Homeodomain protein 2.0 H2.0 FBgn0001235 homothorax hth FBgn0001250 inflated if FBgn0001291 Jun-related antigen Jra FBgn0002306 stranded at second sas FBgn0002526 Laminin A LanA FBgn0002528 Laminin B2 LanB2 FBgn0002542 lodestar lds FBgn0002543 leak lea FBgn0002573 senseless sens FBgn0002609 Enhancer of split m3, helix-loop-helix E(spl)m3-HLH FBgn0002631 Enhancer of split m5, helix-loop-helix E(spl)m5-HLH FBgn0002633 Enhancer of split m7, helix-loop-helix E(spl)m7-HLH FBgn0002733 Enhancer of split mbeta, helix-loop-helix E(spl)mbeta-HLH FBgn0002735 Enhancer of split mgamma, helix-loop-helix E(spl)mgamma-HLH FBgn0002778 minidiscs mnd FBgn0003044 Polycomblike Pcl FBgn0003048 pecanex pcx FBgn0003117 pannier pnr FBgn0003118 pointed pnt FBgn0003145 paired prd FBgn0003169 punt put FBgn0003189 rudimentary r FBgn0003270 absent MD neurons and olfactory sensilla amos FBgn0003328 scab scb FBgn0003429 slowpoke slo FBgn0003430 sloppy paired 1 slp1 FBgn0003435 smooth sm FBgn0003507 serpent srp FBgn0003651 seven up svp FBgn0003716 thickveins tkv FBgn0003720 tailless tll FBgn0003866 teashirt tsh FBgn0003892 patched ptc FBgn0003896 tailup tup FBgn0003900 twist twi FBgn0003975 vestigial vg FBgn0003984 vein vn FBgn0004009 wingless wg FBgn0004054 zerknullt-related zen2 FBgn0004170 scute sc FBgn0004360 Wnt oncogene analog 2 Wnt2 FBgn0004364 18 wheeler 18w FBgn0004368 Protein tyrosine phosphatase 4E Ptp4E FBgn0004370 Protein tyrosine phosphatase 10D Ptp10D FBgn0004567 sloppy paired 2 slp2 FBgn0004606 Zn finger homeodomain 1 zfh1 FBgn0004607 Zn finger homeodomain 2 zfh2 FBgn0004647 Notch N FBgn0004656 female sterile (1) homeotic fs(1)h FBgn0004657 myospheroid mys FBgn0004795 retained retn FBgn0004859 cubitus interruptus ci FBgn0004860 polyhomeotic distal ph-d FBgn0004861 polyhomeotic proximal ph-p FBgn0004878 castor cas FBgn0004897 forkhead domain 96Ca fd96Ca FBgn0004898 forkhead domain 96Cb fd96Cb FBgn0005558 eyeless ey FBgn0005561 shaven sv FBgn0005592 breathless btl FBgn0005612 Sox box protein 14 Sox14 FBgn0005631 roundabout robo FBgn0005634 "" "" FBgn0005658 Ets at 65A Ets65A FBgn0005677 dachshund dac FBgn0005683 pineapple eye pie FBgn0005771 no ocelli noc FBgn0005775 Connectin Con FBgn0010109 deadpan dpn FBgn0010114 hikaru genki hig FBgn0010238 Lachesin Lac FBgn0010263 RNA-binding protein 9 Rbp9 FBgn0010315 Cyclin D CycD FBgn0010341 Cdc42 Cdc42 FBgn0010389 heartless htl FBgn0010395 Integrin betanu subunit Itgbetanu FBgn0010433 atonal ato FBgn0010473 turtle tutl FBgn0010488 NAT1 NAT1 FBgn0010497 Dietary and metabolic glutamate transporter dmGlut FBgn0010575 scribbler sbb FBgn0010583 dreadlocks dock FBgn0010651 lethal (2) 08717 l(2)08717 FBgn0010905 Spinophilin Spn FBgn0011205 fumble fbl FBgn0011224 hephaestus heph FBgn0011259 Sema-1a Sema-1a FBgn0011260 Sema-2a Sema-2a FBgn0011286 Ryanodine receptor 44F Rya-r44F FBgn0011289 Transcription factor IIA L TfIIA-L FBgn0011584 Translocation protein 1 Trp1 FBgn0011592 frazzled fra FBgn0011642 Zyxin Zyx FBgn0011674 inscuteable insc FBgn0011763 DP transcription factor Dp FBgn0011764 Dorsal switch protein 1 Dsp1 FBgn0011837 Tis11 homolog Tis11 FBgn0013272 Gp150 Gp150 FBgn0013303 Neurocalcin Nca FBgn0013576 mustard mtd FBgn0013733 short stop shot FBgn0013981 Histone H4 replacement His4r FBgn0013997 Neurexin IV Nrx-IV FBgn0014007 Protein tyrosine phosphatase 69D Ptp69D FBgn0014020 Rho1 Rho1 FBgn0014037 Su(Tpl) Su(Tpl) FBgn0014343 mirror mirr FBgn0014388 sprouty sty FBgn0015221 Ferritin 2 light chain homologue Fer2LCH FBgn0015222 Ferritin 1 heavy chain homologue Fer1HCH FBgn0015399 kekkon-1 kek1 FBgn0015513 myoblast city mbc FBgn0015558 tweety tty FBgn0015609 Cadherin-N CadN FBgn0015773 Netrin-A NetA FBgn0015774 Netrin-B NetB FBgn0015904 araucan ara FBgn0015919 caupolican caup FBgn0016059 Sema-1b Sema-1b FBgn0016078 wunen wun FBgn0016641 Protein tyrosine phosphatase-ERK/Enhancer of Ras1 PTP-ER FBgn0016660 H15 H15 FBgn0016797 frizzled 2 fz2 FBgn0017590 klingon klg FBgn0019650 twin of eyeless toy FBgn0019985 metabotropic glutamate receptor mGluRA FBgn0020245 tout-velu ttv FBgn0020248 stem cell tumor stet FBgn0020378 Sp1 Sp1 FBgn0020379 Rfx Rfx FBgn0020388 Gcn5 ortholog Gcn5 FBgn0020493 Daughters against dpp Dad FBgn0020620 Related to the N terminus of tre oncogene RN-tre FBgn0020767 Sprouty-related protein with EVH-1 domain Spred FBgn0021764 sidekick sdk FBgn0021767 optomotor-blind-related-gene-1 org-1 FBgn0021818 connector enhancer of ksr cnk FBgn0021873 "" "" FBgn0022984 quaking related 58E-3 qkr58E-3 FBgn0023388 Dynamin associated protein 160 Dap160 FBgn0023423 supernumerary limbs slmb FBgn0024184 unc-4 unc-4 FBgn0024187 sunday driver syd FBgn0024232 gprs gprs FBgn0024248 chico chico FBgn0024251 bobby sox bbx FBgn0024315 Picot Picot FBgn0024728 Slip1 Slip1 FBgn0024921 Transportin Trn FBgn0024987 sister-of-Sex-lethal ssx FBgn0025558 "" CG4101 FBgn0025632 "" CG4313 FBgn0025740 plexin B plexB FBgn0025741 plexin A plexA FBgn0025800 Smad on X Smox FBgn0025806 Ras-associated protein 2-like Rap2l FBgn0025836 Rho GTPase activating protein at 1A RhoGAP1A FBgn0025936 Eph receptor tyrosine kinase Eph FBgn0026058 Ods-site homeobox OdsH FBgn0026063 KP78b KP78b FBgn0026086 Adenosine deaminase acting on RNA Adar FBgn0026160 tonalli tna FBgn0026238 gustavus gus FBgn0026239 GUK-holder gukh FBgn0026323 TGF-beta activated kinase 1 Tak1 FBgn0026562 BM-40-SPARC BM-40-SPARC FBgn0027101 Dyrk3 Dyrk3 FBgn0027499 windei wde FBgn0027515 "" CG7115 FBgn0027561 "" CG18659 FBgn0027570 Neprilysin 2 Nep2 FBgn0027594 draper drpr FBgn0027596 "" CG10249 FBgn0027598 CIN85 and CD2AP orthologue cindr FBgn0028331 lethal (1) G0289 l(1)G0289 FBgn0028369 kin of irre kirre FBgn0028375 heixuedian heix FBgn0028399 TMS1 TMS1 FBgn0028401 Synapse protein 24 Snap24 FBgn0028425 JhI-21 JhI-21 FBgn0028509 Centaurin gamma 1A CenG1A FBgn0028513 "" CG9254 FBgn0028567 robl62A robl62A FBgn0028707 Methyltransferase 2 Mt2 FBgn0028789 Dorsocross1 Doc1 FBgn0028875 nicotinic Acetylcholine Receptor alpha 34E nAcRalpha-34E FBgn0028993 scarecrow scro FBgn0028996 onecut onecut FBgn0028999 nervous fingers 1 nerfin-1 FBgn0029088 dispatched disp FBgn0029123 SoxNeuro SoxN FBgn0029131 death executioner Bcl-2 homologue debcl FBgn0029172 Fad2 Fad2 FBgn0029507 Tetraspanin 42Ed Tsp42Ed FBgn0029508 Tetraspanin 42Ea Tsp42Ea FBgn0029687 Vap-33-1 Vap-33-1 FBgn0029733 "" CG6927 FBgn0029738 "" CG4068 FBgn0029843 Neprilysin 1 Nep1 FBgn0029867 "" CG3847 FBgn0029891 PTEN-induced putative kinase 1 Pink1 FBgn0029939 "" CG9650 FBgn0029944 Downstream of kinase Dok FBgn0030003 "" CG2116 FBgn0030114 "" CG17754 FBgn0030268 Kinesin-like protein at 10A Klp10A FBgn0030286 "" CG1657 FBgn0030318 rhomboid-4 rho-4 FBgn0030366 Ubiquitin-specific protease 7 Usp7 FBgn0030466 "" CG15744 FBgn0030505 NFAT homolog NFAT FBgn0030685 GTPase regulator associated with focal adhesion kinase ortholog (H. sapiens) Graf FBgn0030753 rings lost rngo FBgn0030766 methuselah-like 1 mthl1 FBgn0030812 "" CG8949 FBgn0030816 "" CG16700 FBgn0030864 "" CG8173 FBgn0030930 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 GalNAc-T2 FBgn0031011 "" CG8034 FBgn0031098 "" CG17068 FBgn0031375 earmuff erm FBgn0031534 Sorting nexin 1 Snx1 FBgn0031592 Arginine methyltransferase 2 Art2 FBgn0031645 "" CG3036 FBgn0031725 "" CG14010 FBgn0031760 Tetraspanin 26A Tsp26A FBgn0031850 Thrombospondin Tsp FBgn0031868 "" Rat1 FBgn0031872 interference hedgehog ihog FBgn0031972 WW domain containing oxidoreductase Wwox FBgn0032006 PDGF- and VEGF-receptor related Pvr FBgn0032036 "" CG13384 FBgn0032075 Tetraspanin 29Fb Tsp29Fb FBgn0032196 "" CG5708 FBgn0032243 Kinesin-like protein at 31E Klp31E FBgn0032330 SAM-motif ubiquitously expressed punctatedly localized protein Samuel FBgn0032618 "" CG31743 FBgn0032651 Olig family Oli FBgn0032681 "" CG10283 FBgn0032702 "" CG10376 FBgn0032705 Grip71 Grip71 FBgn0032707 "" CG10348 FBgn0032720 mitochondrial ribosomal protein L13 mRpL13 FBgn0032847 TBP-associated factor 13 Taf13 FBgn0032935 "" CG8678 FBgn0032943 Tetraspanin 39D Tsp39D FBgn0032969 "" CG2528 FBgn0033028 "" CG11665 FBgn0033047 "" CG7882 FBgn0033095 "" CG3409 FBgn0033159 Down syndrome cell adhesion molecule Dscam FBgn0033196 "" CG1358 FBgn0033234 "" CG8791 FBgn0033238 "" CG11165 FBgn0033241 "" CG2915 FBgn0033246 Acetyl-CoA carboxylase ACC FBgn0033252 "" CG12769 FBgn0033310 regular rgr FBgn0033313 Cirl Cirl FBgn0033317 "" CG8635 FBgn0033438 Matrix metalloproteinase 2 Mmp2 FBgn0033636 toutatis tou FBgn0033653 "" CG13192 FBgn0033808 "" CG4627 FBgn0033912 Ribosomal protein S23 RpS23 FBgn0033934 "" CG17385 FBgn0033969 "" CG10202 FBgn0034063 "" CG8389 FBgn0034085 Ptp52F Ptp52F FBgn0034086 "" CG8441 FBgn0034158 "" CG5522 FBgn0034180 Eps15 homology domain containing protein-binding protein 1 Ehbp1 FBgn0034240 Misexpression suppressor of ras 4 MESR4 FBgn0034246 Dicer-2 Dcr-2 FBgn0034389 Multiple C2 domain and transmembrane region protein Mctp FBgn0034392 Major Facilitator Superfamily Transporter 15 MFS15 FBgn0034423 "" CG7229 FBgn0034476 Toll-7 Toll-7 FBgn0034538 "" CG16799 FBgn0034540 Leucine-rich tendon-specific protein Lrt FBgn0034590 Magi Magi FBgn0034723 "" CG13506 FBgn0034782 "" CG12490 FBgn0034783 "" CG9825 FBgn0034946 "" CG3065 FBgn0034971 "" CG3209 FBgn0034999 "" CG3394 FBgn0035101 p130CAS p130CAS FBgn0035103 Vitamin D[[3]] up-regulated protein 1 Vdup1 FBgn0035132 methuselah-like 10 mthl10 FBgn0035142 homeodomain interacting protein kinase hipk FBgn0035150 Rev1 Rev1 FBgn0035161 "" CG13898 FBgn0035238 "" CG12104 FBgn0035357 "" MEP-1 FBgn0035539 slowdown slow FBgn0035623 methuselah-like 2 mthl2 FBgn0035625 Blimp-1 Blimp-1 FBgn0035640 mad2 mad2 FBgn0035643 "" CG13287 FBgn0035645 "" CG5592 FBgn0035798 faulty attraction frac FBgn0035847 methuselah-like 7 mthl7 FBgn0035849 estrogen-related receptor ERR FBgn0035850 Autophagy-specific gene 18 Atg18 FBgn0035954 Dorsocross3 Doc3 FBgn0035956 Dorsocross2 Doc2 FBgn0035983 "" CG4080 FBgn0036007 pathetic path FBgn0036059 nudE nudE FBgn0036147 procollagen lysyl hydroxylase Plod FBgn0036257 Rho GTPase activating protein at 68F RhoGAP68F FBgn0036260 Rhodopsin 7 Rh7 FBgn0036285 twin of eyg toe FBgn0036333 MICAL-like MICAL-like FBgn0036354 Proteome of centrioles 1 Poc1 FBgn0036376 Liprin-beta Liprin-beta FBgn0036411 Sox21a Sox21a FBgn0036451 "" CG9425 FBgn0036493 "" CG7255 FBgn0036494 Toll-6 Toll-6 FBgn0036565 "" CG5235 FBgn0036622 "" CG4753 FBgn0036623 "" CG4729 FBgn0036668 "" CG9715 FBgn0036844 Mitogen-activated protein kinase phosphatase 3 Mkp3 FBgn0036929 "" CG7668 FBgn0037107 "" CG7166 FBgn0037120 "" CG11247 FBgn0037153 olf413 olf413 FBgn0037200 "" CG11109 FBgn0037212 nicotinic Acetylcholine Receptor alpha 80B nAcRalpha-80B FBgn0037350 "" CG2911 FBgn0037465 "" CG1105 FBgn0037472 "" CG10098 FBgn0037481 MAGE MAGE FBgn0037531 "" CG10445 FBgn0037539 "" CG10435 FBgn0037727 "" CG8358 FBgn0037780 "" CG3925 FBgn0037788 "" CG3940 FBgn0037847 SelR SelR FBgn0037853 "" CG14696 FBgn0037856 "" CG4674 FBgn0037876 "" CG4820 FBgn0037894 Ranbp9 Ranbp9 FBgn0037950 Histamine-gated chloride channel subunit 1 HisCl1 FBgn0037956 "" CG6959 FBgn0038188 Arginine methyltransferase 9 Art9 FBgn0038189 Arginine methyltransferase 6 Art6 FBgn0038197 forkhead box, sub-group O foxo FBgn0038237 Phosphodiesterase 6 Pde6 FBgn0038268 "" CG3631 FBgn0038341 "" CG14869 FBgn0038385 "" CG4221 FBgn0038738 "" CG4572 FBgn0038755 Heparan sulfate 6-O-sulfotransferase Hs6st FBgn0038818 Neprilysin 4 Nep4 FBgn0038934 "" Gld2 FBgn0038975 Neurexin 1 Nrx-1 FBgn0039000 "" CG6954 FBgn0039039 lame duck lmd FBgn0039073 "" CG4408 FBgn0039164 "" CG5524 FBgn0039178 "" CG6356 FBgn0039213 atlastin atl FBgn0039355 "" CG4730 FBgn0039431 "" CG6490 FBgn0039487 genderblind gb FBgn0039637 "" CG11880 FBgn0039754 "" CG9747 FBgn0039830 "" CG1746 FBgn0039840 "" CG11340 FBgn0039886 "" CG2003 FBgn0039889 "" CG2219 FBgn0039938 Sox102F Sox102F FBgn0039994 "" CG17082 FBgn0040271 Sulfated Sulf1 FBgn0040318 HGTX HGTX FBgn0040324 Ephrin Ephrin FBgn0040388 brother of ihog boi FBgn0040491 Buffy Buffy FBgn0040765 luna luna FBgn0041087 wunen-2 wun2 FBgn0041111 lilliputian lilli FBgn0041184 Suppressor of cytokine signaling at 36E Socs36E FBgn0042205 "" CG18764 FBgn0042630 Sox21b Sox21b FBgn0042650 disco-related disco-r FBgn0042696 Nuclear factor I NfI FBgn0044328 "" CG32052 FBgn0045852 hamlet ham FBgn0046114 Glutamate-cysteine ligase modifier subunit Gclm FBgn0046247 "" CG5938 FBgn0046687 Trapped in endoderm 1 Tre1 FBgn0046692 Ste20-like kinase Stlk FBgn0050115 Guanine nucleotide exchange factor in mesoderm GEFmeso FBgn0050194 "" "" FBgn0050361 mangetout mtt FBgn0050463 "" CG30463 FBgn0051163 Shal K[+] channel interacting protein SKIP FBgn0051441 "" CG31441 FBgn0051632 senseless-2 sens-2 FBgn0051641 stathmin stai FBgn0051646 "" CG31646 FBgn0051721 Trim9 Trim9 FBgn0051832 "" CG31832 FBgn0052183 Ccn Ccn FBgn0052264 "" CG32264 FBgn0052372 larval translucida ltl FBgn0052475 methuselah-like 8 mthl8 FBgn0052476 methuselah-like 14 mthl14 FBgn0052767 "" CG32767 FBgn0052791 "" CG32791 FBgn0053158 "" CG33158 FBgn0063261 "" CG31275 FBgn0063485 Lasp Lasp FBgn0064123 stargazin-like protein stg1 FBgn0085370 Phosphodiesterase 11 Pde11 FBgn0085408 Shroom Shroom FBgn0085421 Exchange protein directly activated by cAMP ortholog (H. sapiens) Epac FBgn0085432 pangolin pan FBgn0086365 Organic cation transporter 2 Orct2 FBgn0086475 sec3 sec3 FBgn0086675 found in neurons fne FBgn0086680 ventral veins lacking vvl FBgn0086778 giant fibre A gfA FBgn0086899 Tousled-like kinase tlk FBgn0086901 crossveinless c cv-c FBgn0086906 sallimus sls FBgn0086911 rugose rg FBgn0250823 gilgamesh gish FBgn0250876 Semaphorin-5c Sema-5c FBgn0259164 "" CG42269 FBgn0259220 Darkener of apricot Doa FBgn0259221 "" CG42321 FBgn0259227 "" CG42327 FBgn0259228 C3G ortholog (H. sapiens) C3G FBgn0259245 "" CG42343 FBgn0259680 Protein kinase C delta Pkcdelta FBgn0259734 "" CG42388 FBgn0259735 "" CG42389 FBgn0259789 vielfaltig vfl FBgn0259834 outsiders out FBgn0259935 "" CG42458 FBgn0260400 embryonic lethal abnormal vision elav FBgn0260660 multiplexin mp FBgn0260799 Adherens junction protein p120 p120ctn FBgn0260943 RNA-binding protein 6 Rbp6 FBgn0261041 straightjacket stj FBgn0261434 huckebein hkb FBgn0261444 "" CG3638 FBgn0261563 wing blister wb FBgn0261648 spalt major salm FBgn0261723 Dbx Dbx FBgn0261800 LanB1 LanB1 FBgn0261836 Muscle-specific protein 300 Msp-300 FBgn0261930 ventral nervous system defective vnd FBgn0261955 knockdown kdn FBgn0261963 midline mid FBgn0261985 Ptpmeg Ptpmeg FBgn0262103 Salt-inducible kinase 3 Sik3 FBgn0262139 trachealess trh FBgn0262169 magu magu FBgn0262477 Forkhead box P FoxP FBgn0262518 Rab8 Rab8 FBgn0262617 "" CG43143 FBgn0262656 diminutive dm FBgn0262730 "" CG14446 FBgn0262870 axotactin axo FBgn0262872 milton milt FBgn0263006 Calcium ATPase at 60A Ca-P60A FBgn0263490 molting defective mld FBgn0263593 Lipin Lpin FBgn0263603 Zinc-finger protein at 72D Zn72D FBgn0263776 "" CG43693 FBgn0263873 sickie sick FBgn0264089 slit sli FBgn0264270 Sex lethal Sxl FBgn0264442 abrupt ab FBgn0264607 Calcium/calmodulin-dependent protein kinase II CaMKII FBgn0264695 Myosin heavy chain Mhc FBgn0264711 "" CG43980 FBgn0264785 HIF prolyl hydroxylase Hph FBgn0264907 "" CG44098 FBgn0264908 "" pHCl FBgn0264959 Src oncogene at 42A Src42A FBgn0264975 Neuroglian Nrg