Supplemental Table S1a: Alphabetical list of names, gi and accession numbers of PDZ- domain containing used in the ELISA-based PDZ-domain interaction assay. Proteins targeted by siRNA experiments (Figures 5-7) are indicated in bold lettering

Gene Name GI Acc No

AF6 430993 AAC50059 AIPC 12751451 AF338650 ALP 2773059 AF039018 APXL1 13651263 XP_010353 CARD11 12382772 AF322641 CARD14 13129123 NM_024110 CASK 3087815 Y17137 CNK1 3930780 AF100153 Cytohesin binding 3192908 AF068836 Densin 16755892 AF434715 DLG1/SAP97 4758161 NM_004087 DLG2/PSD93/Chapsyn-110 12736552 XM_012060 DLG5 3650451 U61843.1 DVL1 2291005 AF006011 DVL2 2291007 AF006012 DVL3 6806886 NM_004423 EBP50 3220018 AF015926 ELFIN 1 2957144 U90878 ENIGMA 561636 L35240 ERBIN 8923908 NM_018695 FLJ00011 10440352 AK024422 FLJ11215 11436365 XM_006107 FLJ12428 12232472 NM_022783 FLJ12615 10434209 AK022677 FLJ21687 10437836 AK025340 FLJ31349 16550757 AK055911 GORASP 2 13994253 NP_114105 GORASP1 71518807 CH471055 GRIP 1 4539083 AJ133439 GTPase activating enzyme 2389008 AB005666 Guanine exchange factor 6650765 AF117947 HEMBA 1000505 10436367 AK024079 HEMBA 1003117 7022001 AK000997 hShroom 18652858 AB055660 HTRA 3 21326482 AY040094 HTRA 4 12938595 AL576444 INADL 2370148 AJ001306 KIAA0313 7657260 NM_014247 KIAA0316 6683123 AB002314 KIAA0340 14031116 AL590011 KIAA0380 2224700 AB002378 KIAA0382 7662087 NM_015313 KIAA0440 2662160 AB007900

1 Gene Name GI Acc No

KIAA0545 14762850 XM_032278 KIAA0559 3043641 AB011131 KIAA0613 3327039 AB014513 KIAA0858 4240204 AB020665 KIAA0902 4240292 AB020709 KIAA0967 4589577 AB023184 KIAA1202 6330421 AB033028 KIAA1222 6330610 AB033048 KIAA1284 6331369 AB033110 KIAA1389 7243158 AB037810 KIAA1415 7243210 AB037836 KIAA1526 5817166 AL110228 KIAA1620 10047316 AB046840 KIAA1719 1267982 N95487 LIM mystique 12734250 XM_011687 LIM protein 3108092 AF061258 LIM-RIL 1085021 X93510 LIMK1 4587498 AF134379 LIMK2 1805593 D45906 LU-1 22773274 U52111 MAGI 1 3370997 AB010894 Magi 2 2947231 AF038563 MAGI 3 10047344 AB046854 MAST-205 3882334 AB018350 MAST1 4589589 AB023190 MAST3 3043645 AB011133 MAST4 2224546 AB002301 MGC5395 BC012477 BC012477 MINT1 2625024 AF029106 MINT3 3169808 AF029110 MPP1 189785 M64925 MPP2 939884 X82895 MUPP1 3668409 AF093419 NeDLG/SAP102 10863920 NM_021120 Neurabin II 13928135 AJ401189 NOS1/nNOS 642525 U17327 novel PDZ gene 7228177 7228177 novel serine protease 1621243 Y07921 Numb BP 16552333 AK056823 outer membrane 7023825 AK002133 p55T 12733367 XM_004940 PAR3 8037914 AF252293 PAR3L 16903867 AF428250 PAR6 2613011 AF028828 PAR6 beta 13537116 AB044555 PAR6 GAMMA 13537118 AB044556 PDZ-73 71480163 NM_005709

2 Gene Name GI Acc No

PDZK1 2944188 AF012281 PICK1 4678411 AL049654 PIST 98374330 DQ502392 prIL16 1478492 S81601 PSAP 6409315 AF189289 PSD95 3318652 U83192 PSMD9 9184389 BE300702 PTN-3 179912 M64572 PTN-4 190747 M68941 PTPL1 515030 X80289 RGS 3 18644735 NM_130795 RGS12 3290015 AF035152 Rhophilin-1 19697912 AY082588 Rhophilin-like 14279408 AF268032 RIM2 12734165 XM_011672 SEMCAP 3 5889526 AW030770 semcap2 7019938 AK000082 serine protease 2738914 AF020760 Shank 1 6049185 AF141901 Shank 2 22001987 Q9UPX8 Similar to Protein-Tyrosine- Phosphatase Homolog 21595065 BC031614 SIP1 2047327 U82108 SITAC 18 8886071 AF159228 SNPC IIa 20809633 BC029042 SYNTENIN 2795862 AF000652 Syntrophin 1 alpha 1145727 U40571 Syntrophin beta 2 476700 L31529 Syntrophin gamma 1 9507162 NM_018967 Syntrophin gamma 2 9507164 NM_018968 TAX2-like protein 3253116 AC005175 TIAM1 4507500 NM_003253 TIAM2 6912703 NM_012454 TIP1 2613001 AF028823 TIP2 2613003 AF028824 TIP33 2613007 AF028826 TIP43 2613011 AF028828 Unknown PDZ 22382223 BC028375 Vartul 1469875 D63481 X-11 beta 3005559 AF047348 ZO-1 292937 L14837 ZO-2 12734763 XM_005446 ZO-3 10092690 NM_014428

3 Supplemental Table S1b: List of gene names and gi numbers of PDZ-domain ligands (PLs) screened against the PDZs listed in Table 1a.

Abbreviation PL Name gi beta 2 AR Beta-2 114765 CAPON CAPON (carboxyl-terminal PDZ ligand of nNOS) 2895554 DAT Dopamine Transporter (Na+ dependent) 266667 GluR delta-2 delta-2 subunit 2853315 GluR5-2 (rat) glutamate receptor subunit 5-2 204390 mGLUR7 metabotropic glutamate receptor 7 12729188 Glu transporter 3 glutamate transporter 3 11352332 Glycophorin C Glycophorin C 12728038 Kir2.1 Kir2.1 (inwardly rectifying potassium Channel) 8132299 KV1.3 Kv1.3 (inwardly rectifying potassium Channel) 88758565 Neuroligin (20) Neuroligin 1 12729195 Neuroligin (8) Neuroligin 1 12729195 Neuroligin (6) Neuroligin 1 12729195 NMDA R2C NMDA glutamate receptor 2C 1196449 NMDA R2A NMDA glutamate receptor 2A 4504125 NMDA R2B NMDA glutamate receptor 2B 4504127 NMDA R1 NMDA glutamate receptor 1 11496971 NMDA R2D NMDA glutamate receptor 2D 4504131 5HT3a Serotonin receptor 5HT-3A 4504543 5HT2C Serotonin receptor 5HT-2C 12743533 5HT2B Serotonin receptor 5HT-2B 1168220 SSTR2 Receptor 2 12740762 Tat-NR2B9c .007 Tat-NR2B9c Tat-NR2B9c-ADA

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