Supplementary Table 1 Error! Unknown switch argument.

Supplementary Table 1. Transcripts altered greater than 2-fold in cortex of Tg/agrn-/- mice

Fold Gene Description Acc. No. Change

20.9 GTPase activating RANGAP domain-like 1 1441119_at

19.0 transmembrane 7 superfamily member 1 1449671_at

19.0 cell division cycle associated 5 1416802_a_at

18.1 Mus musculus 13 days embryo head cDNA 1454471_at

17.0 t-complex-associated testis expressed 2 1425009_at

15.1 Mus musculus adult male colon cDNA 1454434_at

13.8 Mus musculus transcribed sequence with weak similarity to protein ref:NP_081764.1 1458713_at

Mus musculus transcribed sequence with weak similarity to protein sp:P10266 (H.sapiens) 1459077_at 13.5 POL1_HUMAN Endogenous retrovirus

13.2 origin recognition complex, subunit 4-like (S. cerevisiae) 1431172_at

13.1 runt related transcription factor 1 1422865_at

12.8 potassium channel, subfamily K, member 2 1439657_at

12.5 trimethyllysine hydroxylase, epsilon 1446546_at

12.1 solute carrier family 14 (urea transporter), member 2 1425250_a_at

11.9 cysteine-rich hydrophobic domain 2 1445911_at

11.9 RIKEN cDNA E130115J16 gene 1457775_at

11.5 solute carrier family 26, member 3 1427547_a_at

11.5 EBNA1 binding protein 2 1457668_x_at

11.5 RIKEN cDNA B230325K18 gene 1442354_at

11.5 Mus musculus 10 days neonate cerebellum cDNA 1440757_at

10.8 solute carrier family 1, member 3 1440491_at

10.6 UDP-glucuronosyltransferase 1 family, member 1 1426261_s_at

10.6 Transforming growth factor, beta receptor II (Tgfbr2), transcript variant 2, mRNA 1443115_at

10.6 Zinc finger, SWIM domain containing 6, mRNA (cDNA clone MGC:29327 IMAGE:5025391) 1446682_at

Mus musculus adult male stomach cDNA, RIKEN full-length enriched library, clone:2210411G17 1432668_at 10.5 product:unclassifiable, full insert sequence

10.5 GTP cyclohydrolase 1 1420499_at

10.2 Mus musculus transcribed sequences 1458625_at

10.1 Mus musculus adult male pituitary gland cDNA 1432935_at

Supplementary Table 1 Error! Unknown switch argument.

Fold Gene Description Acc. No. Change

9.9 ADP-ribosyltransferase (NAD+; poly (ADP-ribose polymerase)-like 3 1426210_x_at

9.3 Membrane-associated ring finger (C3HC4) 3 (March3), mRNA 1446422_at

9.2 synaptosomal-associated protein 91 1437817_at

9.2 kynureninase (L-kynurenine hydrolase) 1451903_at

9.1 solute carrier family 35, member A5 1419970_at

9.0 RFamide-related peptide 1421686_at

8.8 popeye domain containing 2 1417806_at

8.4 membrane-associated ring finger (C3HC4) 3 1441643_at

8.0 transmembrane protease, serine 11f 1441981_at

7.9 microfibrillar associated protein 5 1449082_at

7.6 Mus musculus adult retina cDNA 1431522_at

7.5 six transmembrane epithelial antigen of the prostate 1451532_s_at

7.4 Ring finger protein 34, mRNA (cDNA clone MGC:7670 IMAGE:3496314) 1458064_at

7.4 LIM-domain containing, protein kinase (Limk1), mRNA 1456234_at

7.4 ATP-binding cassette, sub-family G (WHITE), member 8 1420656_at

7.3 Mus musculus transcribed sequences 1441099_at

6.9 odd Oz/ten-m homolog 4 (Drosophila) 1447208_at

6.8 Mus musculus adult male testis cDNA 1432345_at

6.6 RIKEN cDNA 4930579E17 gene 1443549_at

6.4 calmin 1451656_at

6.2 Mus musculus 0 day neonate eyeball cDNA 1447262_at

6.0 CD36 antigen 1450883_a_at

6.0 Mus musculus 16 days neonate thymus cDNA 1458126_at

5.8 Mus musculus transcribed sequences 1441092_at

5.7 SET and MYND domain containing 3 (Smyd3), mRNA 1444772_at

5.7 AV369255 RIKEN full-length enriched 1420275_at

5.7 gamma-glutamyltransferase-like activity 1 1418216_at

5.5 Mus musculus transcribed sequences 1458723_at

5.3 GATA zinc finger domain containing 2A 1445239_at

5.3 RIKEN cDNA 2810407C02 gene 1453778_at

5.2 histone 2, H2aa1 1438815_at

5.0 Mus musculus adult male colon cDNA 1430386_at

Supplementary Table 1 Error! Unknown switch argument.

Fold Gene Description Acc. No. Change

4.9 lipocalin 8 1450609_at

4.8 SHP2 interacting transmembrane adaptor 1418751_at

4.7 Mus musculus transcribed sequences 1444609_at

4.7 unnamed protein product; SRY-box containing gene 7 (MGD|MGI:98369, GB|NM_011446 1432495_at

4.6 Mus musculus transcribed sequence with moderate similarity to protein sp:P00722 (E. coli) 1458628_at

4.5 mitochondrial ribosomal protein L52 1455366_at

4.3 Mus musculus adult male small intestine cDNA 1439666_at

4.3 N-myristoyltransferase 2, mRNA (cDNA clone MGC:46936 IMAGE:5253732) 1440433_at

AV090440 Mus musculus tongue C57BL/6J adult Mus musculus cDNA clone 2310050F14, 1420224_at 4.2 mRNA sequence.

4.1 leucyl/cystinyl aminopeptidase 1443907_at

4.1 Mus musculus 10 days neonate cortex cDNA 1447509_at

3.8 serine dehydratase 1424744_at

3.8 vacuolar protein sorting 29 (S. pombe) 1455302_at

3.7 Mus musculus 6 days neonate head cDNA 1454558_at

Myeloid ecotropic viral integration site-related gene 1, mRNA (cDNA clone MGC:13943 1443561_at 3.7 IMAGE:4191098)

3.5 Mus musculus transcribed sequences 1446003_at

3.4 Dedicator of cytokinesis 9, mRNA (cDNA clone MGC:11827 IMAGE:3596515) 1445232_at

3.4 UI-M-DJ2-bwb-i-13-0-UI.s1 NIH_BMAP_DJ2 1441430_at

3.3 AV253518 RIKEN full-length enriched 1438183_x_at

3.3 Mus musculus transcribed sequences 1445092_at

3.2 thioredoxin domain containing 11 1453763_at

3.1 sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D 1453148_at

3.1 coatomer protein complex, subunit gamma 2, antisense 2 1427822_a_at

3.0 Mus musculus adult male liver tumor cDNA 1458435_at

3.0 coagulation factor II (thrombin) receptor 1450852_s_at

3.0 sulfotransferase family, cytosolic, 2B, member 1 1417335_at

3.0 Mus musculus transcribed sequence with weak similarity to protein ref:NP_081764.1 1442384_at

2.9 leucine rich repeat containing 28 1430145_at

2.9 Mus musculus transcribed sequences 1444543_at

2.9 Mus musculus 8 days embryo whole body cDNA, RIKEN full-length enriched library, 1429914_at

Supplementary Table 1 Error! Unknown switch argument.

Fold Gene Description Acc. No. Change

clone:5730566F07 product:enhancer of polycomb homolog 1

2.9 Mus musculus adult male testis cDNA 1445686_at

2.8 solute carrier family 10 (sodium/bile acid cotransporter family), member 1 1443547_at

2.8 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2 1429236_at

2.8 Mus musculus 12 days embryo embryonic body between diaphragm region and neck cDNA 1458892_at

2.8 Histocompatibility 2, class II antigen E beta homolog [Mus musculus], full insert sequence 1456857_at

2.8 Mus musculus transcribed sequences 1442838_at

2.8 solute carrier family 19 (sodium/hydrogen exchanger), member 3 1450348_at

2.8 RBM3; Mus musculus RNA-binding motif protein 3 mRNA, 1422660_at

2.8 cyclin-dependent kinase 2 1416873_a_at

2.8 eukaryotic translation initiation factor 4E 1444010_at

2.7 Mus musculus transcribed sequences 1459105_at

2.7 muscleblind-like 1 (Drosophila) 1440315_at

2.6 expressed sequence AI467484 1436745_at

2.6 Mus musculus 4 days neonate thymus cDNA 1452239_at

2.6 replication factor C (activator 1) 4 1424321_at

2.6 L-amino acid oxidase 1 1417650_at

2.5 procollagen, type V, alpha 2 1422437_at

2.5 C. elegans ceh-10 homeo domain containing homolog 1419628_at

2.5 immunity-associated protein 1449988_at

2.5 RIKEN cDNA 9930116P15 gene 1420221_at

2.5 RIKEN cDNA 1110034A24 gene 1454968_at

2.5 eukaryotic translation initiation factor 2-alpha kinase 2 1440866_at

2.5 cyclin A2 1417911_at

2.5 601777133F1 NCI_CGAP_Lu29 Mus musculus cDNA clone 1453734_at

2.5 Mus musculus transcribed sequences 1459844_at

Mus musculus transcribed sequence with weak similarity to protein ref:NP_081764.1 1441399_at 2.5 (M.musculus)

2.5 BCL2-like 11 (apoptosis facilitator) 1435448_at

2.5 Mus musculus cDNA clone MGC:8099 IMAGE:3588650, complete cds. 1426074_at

2.5 RIKEN cDNA 5830415L20 gene 1449950_at

2.5 Mus musculus transcribed sequences 1442913_at

Supplementary Table 1 Error! Unknown switch argument.

Fold Gene Description Acc. No. Change

2.4 interleukin 1 beta 1449399_a_at

2.4 carboxypeptidase X 1 (M14 family) 1448901_at

2.4 Mus musculus transcribed sequences 1444946_at

2.4 cold inducible RNA binding protein 1416332_at

2.4 nuclear factor I/B 1434101_at

2.4 Caspase 7, mRNA (cDNA clone MGC:5872 IMAGE:3600155) 1434099_at

2.4 similar to ribosomal protein L18a 1458465_at

2.4 protein kinase C, eta 1422079_at

2.4 phosphoseryl-tRNA kinase 1455953_x_at

2.4 smoothened homolog (Drosophila) 1427049_s_at

Mus musculus transcribed sequence with weak similarity to protein pir:I58401 (M.musculus) 1460072_at 2.3 I58401 protein-tyrosine kinase (EC 2.7.1.112) JAK3 - mouse

2.3 SEC22 vesicle trafficking protein-like 2 (S. cerevisiae) (Sec22l2), mRNA 1441696_at

2.3 Mus musculus 12 days embryo spinal ganglion cDNA 1446338_at

2.3 ring finger protein 125 1429399_at

2.3 Mus musculus transcribed sequences 1447124_at

2.3 RIKEN cDNA 4930571B16 gene 1432050_at

2.3 cytotoxic T lymphocyte-associated protein 2 alpha 1448471_a_at

Mus musculus transcribed sequence with weak similarity to protein ref:NP_081764.1 1443330_at 2.3 (M.musculus)

2.3 kalirin, RhoGEF kinase 1429796_at

2.3 kinesin family member 22 1437716_x_at

2.2 galactosamine (N-acetyl)-6-sulfate sulfatase 1448744_at

2.2 WD repeat domain 6 1415770_at

2.2 retroviral integration site 2 1424143_a_at

2.2 RIKEN cDNA B230342M21 gene 1452914_at

2.2 Nucleolin, mRNA (cDNA clone MGC:6363 IMAGE:3495665) 1442404_at

2.2 Mus musculus adult male diencephalon cDNA 1459321_at

2.2 target of myb1-like 1 (chicken) 1451117_a_at

2.2 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 1456888_at

2.2 Mus musculus transcribed sequences 1446012_at

2.2 BB458543 RIKEN full-length enriched 1441881_x_at

Supplementary Table 1 Error! Unknown switch argument.

Fold Gene Description Acc. No. Change

2.2 alanine-glyoxylate aminotransferase 2-like 1 1452975_at

2.2 Mus musculus transcribed sequences 1440123_at

2.2 RNA binding motif protein 21 1451106_at

2.2 Mus musculus transcribed sequences 1444441_at

2.2 AV332575 RIKEN full-length enriched 1447774_x_at

2.2 RIKEN cDNA 6330500D04 gene 1458202_at

2.2 collagen, type IV, alpha 3 (Goodpasture antigen) binding protein 1449847_a_at

2.2 RAN binding protein 2 1445883_at

2.1 Mus musculus 12 days embryo head cDNA 1429841_at

2.1 RIKEN cDNA A630072M18 gene 1427081_at

2.1 BB556978 RIKEN full-length enriched 1456009_x_at

2.1 RIKEN cDNA 1110065L07 gene 1428273_at

2.1 expressed sequence AI894139 1433619_at

2.1 3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1 1434913_at

2.1 Mus musculus adult male hippocampus cDNA 1454510_at

2.1 diazepam binding inhibitor 1438093_x_at

2.1 Mus musculus transcribed sequences 1443833_at

2.1 A kinase (PRKA) anchor protein (yotiao) 9 1447913_x_at

2.1 splicing factor, arginine/serine-rich 2 (SC-35) 1427504_s_at

2.1 spinocerebellar ataxia 7 homolog (human) 1442186_at

2.1 NIP21 (Nip21) 1441989_at

2.0 chromodomain helicase DNA binding protein 2 1445843_at

-2.1 Mus musculus transcribed sequences 1455638_at

-2.1 Mus musculus transcribed sequence with weak similarity to protein pir:I58401 (M.musculus) 1457792_at

-2.1 Endonuclease G-like 1 (Endogl1), mRNA 1455525_at

Mus musculus transcribed sequence with weak similarity to protein ref:NP_081764.1 1458235_at -2.1 (M.musculus)

-2.2 Mus musculus adult male urinary bladder cDNA 1445101_at

-2.2 Mus musculus 0 day neonate lung cDNA 1446569_at

-2.2 mitochondrial translational release factor 1-like 1438025_at

-2.2 phosphorylase kinase gamma 1422315_x_at

-2.2 N-myc (and STAT) interactor 1425719_a_at

Supplementary Table 1 Error! Unknown switch argument.

Fold Gene Description Acc. No. Change

-2.2 Mus musculus 10 days neonate head cDNA 1430345_at

-2.3 protein kinase C, alpha 1427562_a_at

-2.3 RIKEN cDNA 2700016E08 gene 1438051_at

-2.3 chemokine (C-X-C motif) ligand 11 1419698_at

-2.3 nuclear factor, interleukin 3, regulated 1418932_at

-2.4 hypothetical protein C230004F18 1445854_at

-2.4 mitogen activated protein kinase kinase 7 1421416_at

-2.4 RIKEN cDNA 4732486I23 gene 1427151_at

-2.5 fibulin 2 1423407_a_at

Mus musculus cDNA clone 5830408C01 3' similar to X74953 M.musculus ETL-2 mRNA, mRNA 1459868_x_at -2.5 sequence

-2.5 RIKEN cDNA 1110014F24 gene 1428781_at

-2.6 tripartite motif protein 25 1419879_s_at

-2.6 death-associated kinase 2 1451453_at

-2.6 keratin complex 1, acidic, gene 5 1427751_a_at

-2.6 Mus musculus adult male testis cDNA 1444710_at

-2.7 immediate early response 5 1417613_at

-2.7 ubiquitin-conjugating enzyme E2T (putative) 1422462_at

-2.7 Mus musculus adult male testis cDNA 1431975_at

-2.7 agrin 1426670_at

-2.8 aldehyde oxidase 1 1419435_at

-3.0 MKIAA4006 protein 1446356_at

-3.0 Mus musculus 2 days neonate thymus thymic cells cDNA 1434929_at

AV366661 RIKEN full-length enriched, 16 days embryo lung Mus musculus cDNA clone 1447915_x_at -3.1 8430422K07 3', mRNA sequence.

-3.2 RIKEN cDNA 2700045P11 gene 1453428_at

-3.4 Mus musculus adult male corpus striatum cDNA 1442754_at

-3.5 aquarius 1430275_a_at

-3.5 GTP cyclohydrolase 1 1429692_s_at

-3.6 RIKEN cDNA 2610037M15 gene 1430496_at

-3.6 dispatched homolog 2 (Drosophila) 1446729_at

-3.7 adenylate kinase 1 1423988_at

Supplementary Table 1 Error! Unknown switch argument.

Fold Gene Description Acc. No. Change

-3.7 phosphatidylinositol 3-kinase catalytic delta polypeptide 1458321_at

-3.7 solute carrier family 39 (zinc transporter), member 2 1443163_at

-4.0 Mus musculus adult male testis cDNA 1430398_at

-4.5 KH-type splicing regulatory protein 1452690_at

-4.7 hyaluronan synthase 2 1449169_at

-4.7 Mus musculus adult male testis cDNA 1432932_at

-5.1 TAF7-like RNA polymerase II 1420433_at

-5.1 heparanase 1433930_at

-5.1 hydroxyacid oxidase 1, liver 1420420_at

-5.9 Mus musculus adult male testis cDNA 1433003_at

-5.9 Mus musculus transcribed sequences 1441289_at

-6.1 cathepsin L 1457724_at

-6.2 interleukin 1 receptor, type II 1419532_at

-6.3 RIKEN cDNA 2610001J05 gene 1448002_x_at

-7.0 Mus musculus transcribed sequences 1444919_at

-7.4 ankyrin repeat and BTB (POZ) domain containing 2 1444771_at

-7.5 RIKEN cDNA D730048I06 gene 1422004_at

-7.6 WW domain containing transcription regulator 1 (Wwtr1), mRNA 1458655_at

-8.0 Ras association (RalGDS/AF-6) domain family 1 1456994_at

-8.2 ectodysplasin A2 isoform receptor 1440085_at

-8.3 BB809910 RIKEN full-length enriched, lung RCB-0558 LLC cDNA. 1453561_x_at

-8.4 regulator of G-protein signaling 9 1426033_at

-8.5 molybdenum cofactor synthesis 1 1425004_s_at

-8.6 chemokine (C-X-C motif) ligand 1 1419209_at

-8.6 UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6 1435252_at

-8.8 pleckstrin homology-like domain, family A, member 2 1417837_at

-8.9 Mus musculus transcribed sequences 1445335_at

-9.5 Mus musculus transcribed sequences 1444261_at

-10.1 RIKEN cDNA 4933413G11 gene 1430009_at

-10.9 immunoglobulin superfamily, member 1 1447702_x_at

-10.9 insulin promoter factor 1, homeodomain transcription factor 1422173_at

-11.0 BB181468 RIKEN full-length enriched, adult male hypothalamus Mus musculus cDNA clone 1442649_at

Supplementary Table 1 Error! Unknown switch argument.

Fold Gene Description Acc. No. Change

A230091H21 3', mRNA sequence.

-11.3 Mus musculus anti-DNA immunoglobulin light chain variable region, clone 4B2, partial cds. 1427856_a_at

Leucine rich repeat containing 8 family, member C, mRNA (cDNA clone MGC:36625 1439469_at -11.4 IMAGE:5353064)

-11.5 Mus musculus adult male testis cDNA 1433238_at

-12.1 Mus musculus transcribed sequences 1444922_at

-13.2 RIKEN cDNA 1110006O17 gene 1450404_at

-13.3 T-box 21 1449361_at

-16.3 Anthrax toxin receptor 2, mRNA (cDNA clone IMAGE:3484366) 1446249_at

-16.4 ring finger protein 17 1425708_at

-16.5 Mus musculus transcribed sequences 1448088_at

-16.5 zinc finger protein 473 1457078_at

-18.9 Mus musculus 13 days embryo male testis cDNA 1433373_at

-21.7 ribosomal protein S6 1435962_at

-23.6 kinesin family member 13B 1433248_at

List of genes whose expression was significantly changed at least 2 fold in cortices of 4 week- old Tg/agrn-/- mice. Upregulated genes are given numbers above 2; downregulated genes are given numbers below -2. Note that agrin transcripts are strongly downregulated in Tg/agrn-/- mice as would be expected.