Table 3 NS-ID Gene Interactions Interactions were determined using 4 databases: BioGRID (www.thebiogrid.org), HPRD (www.hprd.org), String (www.string-db.org) and IntAct (http://www.ebi.ac.uk/intact). Interactions from all 4 databases are recorded for each gene. For each interaction identified on these websites there is a link to the appropriate publication for that interaction. In BioGRID, the publication can be found by clicking on the “publication” link. For HPRD the publication can be found by clicking on the “experiment type” next to each interaction. For String, clicking on the “experiments” link and then on the “details” for the interaction brings up the published abstract. For IntAct, the EBI identification number has been provided for each protein, and this can be queried on the IntAct database to find the publication information. Interactants not found in these databases have been cited independently. *Interactions have been identified in animal studies

ACSL4

SPG20 (EBI-2643801)

AFF2/FMR2

GRB2 (EBI-1964238); NCK1 (EBI-1968993); PLCG1 (EBI-1971165); MAPK14 (EBI-1959498)

AGTR2

AGT; AGTRAP; ACE; MTUS1; TIMP3 (EBI-1749967); GNAI2*; GNAI3*; ZBTB16; PIK3CB; ERBB3

AP1S2

AP1G2 (EBI-516314); AP1G1 (EBI-516318); AP1S1 (EBI-1073310); GGA3

ARHGEF6

GIT1; PKLR; BMPR1B; PAK1-3; ARHGEF7; SMAD1-3; TGFBR1; TGFBR2; PARVB; CAPNS1; CDC42; EPHB2; YWHAG; SH2D1A; ADAM15;

ARX

None known

ATRX

DAXX (EBI-371424); NEK1 (EBI-695931); PTN (EBI-731356); HDAC1; HDAC4; RAD51; ATN1; FAM190B (EBI-731347); EZH2; EIF4A2 (EBI-1069160); MECP2*; SMC1A; CBX5; PTPN4; H3F3A; H3F3B; KIAA1377; LUC7L2; KIAA1128

BRWD3

UBXD7 (EBI-2009865)

CASK

LIN7A; DLG1; TBR1 (EBI-1216781); KCNJ12 (EBI-704591); APBA1; PARK2; RPH3A (EBI-1216824); F11R; ATP2B4; SDC1-4; DLG4; TSPYL2; ID1 (EBI-1215556); KNCJ4 (EBI-706129); NPHS1; CNTNAP2; CNTNAP4; HGS; SPATA2; UIMC1 (EBI-2515432); LIN7C; EPB41 (EBI-1219323); C16ORF70; CD2AP; FCHSD2 (EBI-1215794); LIN7B; EPS8; GRIK2; RAB3A; CASK; KCNJ2 (EBI-706107); DLG1; CADM1; NRXN1-3; DFNB31; CASKIN1; TANC1; GRIN2A; KCNA4; GLS2; NF1; HTR2C; ARHGEF7; KIRREL3 (Bhalla et al. 2008)

CC2D1A

CHMP4A; CHMP4C

CDH15

CTNNA1; CTNNB1; JUP; GNA12; BOC; ARVCF; CDON; CDH9; CDH7

CRBN

DDB1* (EBI-2559059); CSN6 (EBI-2510262); CUL4A

DLG3

GRIN2A; GRIN2B; EXOC4; KNCJ12 (EBI-704591); APC; PTK2B; DLG4; SYNGAP1; GDA; CRIPT; GRIN2C; SSCR2*; GUCY1A2; NLGN2; ATP2B4; NLGN1; GRIK2, DLGAP1; NLGN3; ATP2B2; GRIK5; SEMA4C; EXOC7; KRT85 (EBI-1085330); KRT34 (EBI-1077921); KRT35; KRT31 (EBI-1082542); ERBB4 (EBI-80454); CAMK2A (EBI-1068669); CUL2 (EBI-1081586); ANXA1 (EBI-1077519); S100A3 (EBI-1081429); EXOC3; HIST1H2BC; KLHDC3 (EBI-1081381); KRT82 (EBI-1084718); LRP2; CALM1; CNKSR2; KIF1B; MAPK12; KCNA4; SCN4A; ABCA1 (EBI-784253); LPHN1; DLG1; LIN7A; GRIN1; DLGAP4; CACNG2; SCN5A; GLS2; KCNJ2; DLGAP3; GRIK5; PAEP; SCN4A; IDUA (EBI-737171); INSM1 (EBI-737174); MORN2 (EBI-737180); PPP1R14A* (EBI-776423); DLGAP2* (EBI-389360); MDH1 (EBI-735148); SF3B3 (EBI-737189); LRFN2* (EBI-877173); PLK2 (EBI-735154); RBP5 (EBI-737168); TRIM41 (EBI-737192); HAP1 (EBI-732554); SCN2A (EBI-737186); RAB31 (EBI-737183); MCM2 (EBI-732557); B3GNT8 (EBI-737165);

DOCK8

CDC42; RAC1; RHOJ; RHOQ

FGD1

CDC42; ELMO1; ABP1; CTTN; RHOA; RHOG; RHOU; RHOC; RAC2; IFNB1

FTSJ1

DMWD; FBL; NOP58;

GDI1

RAB1B; RAB6A; RAB3B; RAB9A; RAB27A; PSEN1; RHOH; CDC42; RAC2; RHOA; RABAC1; EPB41; SPOP

GRIK2

DLG4; SDCBP; PICK1; DLG1; GRIK5; GRIP1; GRIA1; GRIA2; GRID1; DLG3; CDH2; CTNNB1; CASK; GRIK2; GRIK4; CTNND1; PRKAA1; LIN7B; GRID2; GOLM1 (EBI-736856); GPAA1 (EBI-736877); LRSAM1 (EBI-737066); MLF1 (EBI-735133)

HUWE1

CDKN2A (EBI-625921); UBL4A (EBI-2515855); FAF2 (EBI-2009967); UBE2E3 (EBI-2339614); GIYD2 (EBI-2372444); P53 EBI-626140); VCPIP1 (EBI-2513235); USP7 (EBI-2513133); MYC (EBI-1237540); UBXN1 (EBI-2010040); CDC6; USP49 (EBI-2512828); USP50; SMAD2; CCL1; RNF11; SMAD9; MCL1; ATM

IL1RAPL1

NCS-1/FREQ; DLG4 (Pavlowsky et al. 2010); CFTR (EBI-1171098)

JARID1C/KDM5C

HIST2H3A; SMAD3; RNF2, MAX, REST NCOR1, HDAC1, HDAC2, E2F6, RING1, CBX3;

KIRREL3

CASK (Bhalla et al. 2008)

MAGT1

None known

MBD5

None known

MECP2

SIN3A; LBR; HDAC1; PRPF40A; SPI1; PRPF40B; SKI; DNMT; CDKL5; RBPJ; YBX1; CBX5; SMARCA2; SMARCB1; ATRX*; RCOR1; GTF2B; SUV39H3; HIST2H3A; SIN3B; NCOR1; SMARCE1

NLGN4X

DLG4; DLGAP2

OPHN1

RHOA; RAC1; CDC42

PAK3

RAC1; RAF1; ARHGEF6; ARHGEF7; SYN1; PXN; MYO6; GIT2; NCK1; CDC42

PQBP1

POU3F2; POLR2A; EEF1A1 (EBI-730579) ATXN1; MED31 (EBI-730576); SF3A2; TXNL4A; WBP11 (EBI-956742); RIF1 (EBI-732938); C14ORF1 (EBI-735456); RAB8A (EBI-737426); C1ORF103

PRSS12

None known

PTCHD1

None known

RPS6KA3

MAPT; MAPK1; MAPK3; PLD1; BAD; HIST3H3; CREB1; FGF2; NR4A1; SYT3; KRT18; CREBBP; MAPK14; PEA15; IGF1; PDPK1; GSTK1 (EBI-1079890); CSNK2B (EBI-1371784)

SHANK2

DLGAP1-4; DNM2; ARHGEF7; CTTN; SSTR2*; DLG4; DYNLL1; DYNLL2; MYO5A; LPHN1; LPHN2; BAI2; SLC9A3; BAIAP2; NCK1 (EBI-1968244); PLCG1 (EBI-1971189); PIK3R1 (EBI-1969713); PPP1R14A* (EBI-776423); SRC (EBI-1960646); GRB2 (EBI-1963670); GRIN2B* (EBI-770442); GRIN1 (EBI-396959); HOMER/Ves1 (Hayashi et al. 2009); CRK (EBI-1959944)

SHROOM4

MYO6; MYO1A; MYO1C; MYO9B; CORO1A; CD2AP

SLC6A8

CD59

STXBP1

STX1A; STX1B; STX2-4; STX5* SYTL4; STX1B2; SNAP25; ABPA1/Mint1; APBA2*; DLG4*; TUBB2A; TUBA4A; MAPT; HGS; DOC2A; PLD1; CDK5R1; NEFH; CDK5; USO1; PRKCA; PRKCB1; PRKCG

SYNGAP1

ULK1; DLG4; DLG3; ULK2; CAMK2A; MPDZ; DLG3; DLG4; GRIN2A; GRIN2B; GRIN1; TRIP6; PDGFRB; KDR

SYP

GRB2; VAMP2; SIAH1; SIAH2; AP1G1; STX1A; EPOR

TSPAN7

KPTN; FYTTD1

TRAPPC9

TRAPP complex; IKBKB; MAP3K14

TUSC3

PPP1CA

UPF3B

UPF1 (EBI-536644); UPF2 (EBI-374193); RBM8A; NCBP1 (EBI-1776148); HBB; USP21 (EBI-2512177); EIF6; EIF4A3 (EBI-464796); UPF3A; TTC19 (EBI-374205); MCRS1 (EBI-374202); EIF4G1 (EBI-464801); ITGB3BP (EBI-732256)

ZNF41

SMAD2

ZNF674

None known

ZNF711

PHF8 (Kleine-Kohlbrecher et al. 2010)

ZNF81

None known