Related Genes and Mossy Fibre Length in Dentate Granule Cells from Adult Hud Overexpressor Mice

ASN NEURO 3(5):art:e00070.doi:10.1042/AN20110015 RESEARCH ARTICLE

Increased expression of axogenesis- related genes and mossy fibre length in dentate granule cells from adult HuD overexpressor mice

Nora I Perrone-Bizzozero1, Daniel C Tanner2, Joanna Mounce and Federico Bolognani3 Departmemt of Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA

Cite this article as: Perrone-Bizzozero NI, Tanner DC, Mounce J and Bolognani F (2011) Increased expression of axogenesis-related genes and mossy fibre length in dentate granule cells from adult HuD overexpressor mice. ASN NEURO 3(5):art:e00070.doi:10.1042/AN20110015 Key words: axonal outgrowth, dentate granule cell, gene profiling, HuD, post-transcriptional mechanisms, RNA-binding protein.

Supplementary Tables S1 and S2 are on the following pages

1 To whom correspondence should be addressed (email: [email protected]). 2 Present address: Department of Biomedical Genetics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA 3 Present address: Novartis Pharma AG, Basel, Switzerland. Abbreviations: aCaMKII, a-Ca2+/calmodulin-dependent protein kinase II; ARE, AU-rich element; ARED, ARE database; CP, choroid plexus; Dcx, doublecortin; DGC, dentate granule cell; DIG, digoxigenin; EST, expressed sequence tag; FISH, fluorescence in situ hybridization; GAP-43, growth-associated protein 43; GAPDH, glyceraldehyde-3- phosphate dehydrogenase; GO, gene ontology; GRE, GU-rich element; IPA, ingenuity pathway analysis; IPB, infrapyramidal bundle; ISH, in situ hybridization; KO, knockout; LCM, laser capture microscopy; Mtap1b, microtubule-associated protein 1b; NIH, National Institutes of Health; PFA, paraformaldehyde; PPF, paired-pulse facilitation; qRT– PCR, quantitative reverse transcription–PCR; RNA-IP, RNA-immunoprecipitation; SMA, spinal muscular atrophy; SPB, suprapyramidal bundle; T3,3,39,5-tri-iodothyronine; T4, thyroxine; TTR, transthyretin; 39-UTR, 39-untranslated region; WT, wild-type. E 2011 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial Licence (http:// creativecommons.org/licenses/by-nc/2.5/) which permits unrestricted non-commercial use, distribution and reproduction in any medium, provided the original work is properly cited.

asnneuro.org / Volume 3 (5) / art:e00070 hc emt netitdnncmeia s,dsrbto n erdcini n eim rvddteoiia oki rprycited. properly is work original the provided medium, any in reproduction and distribution use, non-commerical unrestricted permits which E 01TeAuthor(s) The 2011 Table S1 HuD DGC up-regulated transcripts and 3’ UTR motif analysis

Fold 39 UTR OL Type Type Type Type Type Type Motif Motif Motif Validated others and Perrone-Bizzozero N.I. Systematic change P-value Gene symbol Ensembl gene ID length ARED AUUUA AUUUA I IIA IIB IIC IID IIE U-rich GRE 1 2 3 target? Gene description

1455913_x_at 57.04 0.000774 Ttr ENSMUSG00000061808 586 0 0 0 0000001400 0 1 Transthyretin 1454608_x_at 39.52 0.011 Ttr ENSMUSG00000061808 586 0 0 0 0000001400 0 1 Transthyretin hsi nOe cesatcedsrbtdudrtetrso h raieCmosAtiuinNnCmeca iec (http://creativecommons.or Licence Non-Commercial Attribution Commons Creative the of terms the under distributed article Access Open an is This 1451580_a_at 32.01 0.0127 Ttr ENSMUSG00000061808 586 0 0 0 0000001400 0 1 Transthyretin 1459737_s_at 23.4 0.00189 Ttr ENSMUSG00000061808 586 0 0 0 0000001400 0 1 Transthyretin 1433474_at 4.827 0.00000142 Edil3 ENSMUSG00000034488 3403 1 16 0 0000014300 1 0 Yes EGF-like repeats and discoidin I-like domains 3 1450577_at 4.465 0.016 Sstr3 ENSMUSG00000044933 2244 0 1 0 0000000 00 0 0 Somatostatin receptor 3 1451246_s_at 4.174 0.0037 Aurkb ENSMUSG00000020897 603 0 1 0 0000000 00 0 0 Aurora kinase B 1441909_s_at 3.869 0.00777 9530066K23Rik ENSMUSG00000020411 1991 0 3 0 0000000 02 0 0 RIKENcDNA 9530066K23 gene 1449011_at 3.778 0.0345 Slc12a7 ENSMUSG00000017756 1818 1 3 1 0001014 01 0 0 Solutecarrierfamily 12, member 7 1441946_at 3.409 0.00498 Itih5 ENSMUSG00000025780 4946 1 10 0 0000014 17 0 0 Inter-alpha (globulin) inhibitor H5 1438387_x_at 3.396 0.00591 Top3b ENSMUSG00000022779 1325 0 0 0 0000000 00 0 0 Topoisomerase (DNA) III beta 1427008_at 3.312 0.0169 4732452J19Rik ENSMUSG00000034177 1340 0 3 0 1000000 01 0 0 RIKENcDNA 4732452J19 gene 1418280_at 3.285 0.032 Klf6 ENSMUSG00000000078 3110 0 7 0 0000004701 5 1 Yes Kruppel-like factor 6 1459205_at 3.075 0.00746 Cpeb1 ENSMUSG00000025586 1315 0 5 0 0000009 00 0 0 Yes Cytoplasmic polyadenylation element binding protein 1 (Cpeb1), mRNA 1421964_at 2.915 0.0209 Notch3 ENSMUSG00000038146 1000 0 2 0 0000002105 0 0 Yes Notch gene homologue 3 (Drosophila) 1435858_at 2.88 0.0098 Tmem215 ENSMUSG00000046593 2536 1 11 0 0000004401 110 Transcribed locus 1458458_at 2.856 0.0273 Slfn5 ENSMUSG00000054404 1237 0 4 0 0000000 0140 0 Schlafen 5 1429011_x_at 2.826 0.0386 SNRNP70 ENSMUSG00000063511 143 0 1 0 0000000 00 0 1 U1small nuclear ribonucleoprotein polypeptide A 1452993_at 2.823 0.0103 5430416O09Rik ENSMUSG00000028475 3133 0 3 0 0000001711 3 1 RIKENcDNA 5430416O09 gene 1453563_at 2.809 0.0259 1110025F24Rik ENSMUSG00000063445 208 0 0 0 0000002 00 0 0 RIKENcDNA 1110025F24 gene 1435306_a_at 2.796 0.0287 Kif11 ENSMUSG00000012443 1469 0 2 0 0000005 01 0 0 Kinesin family member 11 1446819_at 2.773 0.0374 Lrp1b ENSMUSG00000049252 1686 0 4 0 0000000 00 0 0 Lowdensity lipoprotein-related protein 1B (deleted in tumors) (Lrp1b), mRNA 1434430_s_at 2.715 0.0485 Adora2b ENSMUSG00000018500 728 0 3 0 0000000 00 0 0 Adenosine A2b receptor 1456976_at 2.71 0.0134 Wnt5a ENSMUSG00000021994 4507 3 10 0 00000096610163 YesWingless-related MMTV integration site 5A 1445824_at 2.708 0.00132 Zfp458 ENSMUSG00000055480 1197 0 2 0 0000000 00 0 0 Yes Zinc finger protein 458 1451415_at 2.617 0.0231 1810011O10Rik ENSMUSG00000056313 960 1 1 0 0000013500 3 3 Yes RIKEN cDNA 1810011O10 gene 1430402_at 2.611 0.0439 Sucla2 ENSMUSG00000022110 694 1 2 0 0000000 00 0 0 Succinate-coenzyme A ligase, ADP-forming, beta subunit 1420689_at 2.573 0.0308 4933415F23Rik ENSMUSG00000073730 1297 0 1 0 0000000 01 0 0 RIKENcDNA 4933415F23 gene Gene 1456936_at 2.559 0.0367 Cabp4 ENSMUSG00000024842 562 0 0 0 0000000 00 0 0 Calciumbindingprotein4 1456742_x_at 2.555 0.0134 Tm9sf2 ENSMUSG00000025544 888 0 4 0 0000000 00 0 0 Yes Transmembrane 9 superfamily member 2 1431257_at 2.551 0.0334 6230409E13Rik ENSMUSG00000028246 1164 0 0 0 0000001200 0 0 Yes RIKEN cDNA 6230409E13 gene 1429462_at 2.549 0.0365 Slc25a32 ENSMUSG00000022299 1779 0 9 0 0000002 10 0 0 Solutecarrierfamily 25, member 32 1419486_at 2.538 0.00644 Foxc1 ENSMUSG00000050295 1766 0 3 0 0000007 10 0 0 Yes Forkhead box C1 1459116_at 2.538 0.0327 Ncam2 ENSMUSG00000022762 2492 0 11 0 0000003100 2 0 Neural cell adhesion molecule 2 (Ncam2), mRNA 1419193_a_at 2.535 0.0109 Gmfg ENSMUSG00000060791 103 0 0 0 0000000 00 0 0 Yes Glia maturation factor, gamma 1443782_x_at 2.525 0.0255 Cyp20a1 ENSMUSG00000049439 771 0 0 0 0000004100 6 0 Yes Cytochrome P450, family 20, subfamily A, polypeptide 1 1440745_at 2.49 0.0267 C130091E20 ENSMUSG00000039410 4785 1 5 0 0000007213 141 Hypothetical protein C130091E20 1422637_at 2.472 0.0171 Rassf5 ENSMUSG00000026430 2294 0 4 0 1000009 00 4 0 Yes Ras association (RalGDS/AF-6) domain family 5 1429934_at 2.441 0.0336 4930502E18Rik ENSMUSG00000055555 584 0 2 0 0000002260 6 0 Yes RIKEN cDNA 4930502E18 gene 1456312_x_at 2.436 0.0307 Gsn ENSMUSG00000026879 231 0 0 0 0000009 00 1 0 Gelsolin 1442631_at 2.424 0.022 2700070H01Rik ENSMUSG00000054763 2470 0 6 0 0000017 00 1 0 RIKENcDNA 2700070H01 gene 1448768_at 2.385 0.0236 Mog ENSMUSG00000076439 758 0 0 0 0000000 02 0 0 Myelin oligodendrocyte glycoprotein 1433742_at 2.375 0.0441 Ankrd15 ENSMUSG00000032702 913 0 1 0 0000000 00 0 0 Ankyrin repeat domain 15 1418166_at 2.37 0.0379 Il12rb1 ENSMUSG00000000791 663 0 0 0 0000000 00 0 0 Interleukin 12 receptor, beta 1 1427829_at 2.358 0.0467 Abcd4 ENSMUSG00000021240 560 0 2 0 1000000 00 0 0 ATP-binding cassette, sub-family D (ALD), member 4 1428821_at 2.33 0.0293 Agpat2 ENSMUSG00000026922 992 0 0 0 0000000 00 0 0 1-Acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta) 1442697_at 2.295 0.00212 Ipo11 ENSMUSG00000042590 1192 0 5 0 2000000 00 0 0 Importin 11, mRNA (cDNA clone MGC:39010

g/licenses/by-nc/2.5/) IMAGE:5364208) 1418706_at 2.292 0.049 Slc38a3 ENSMUSG00000010064 773 0 0 0 0000000 04 0 0 Solutecarrierfamily 38, member 3 1446577_at 2.286 0.0448 Pde4b ENSMUSG00000028525 1920 0 3 0 0000000 02 0 0 Yes C57BL/6J phosphodiesterase 4B (Pde4b) 1449009_at 2.277 0.0358 Tgtp ENSMUSG00000078921 1302 0 1 0 0000000 01 0 0 T-cell specific GTPase 1448105_at 2.261 0.0162 Prm2 ENSMUSG00000038015 187 0 0 0 0000000 00 0 0 Protamine 2 1426621_a_at 2.258 0.0259 Ppp2r2b ENSMUSG00000024500 459 0 1 0 0000000 00 0 0 Protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform 1443993_at 2.257 0.047 Zc3h12a ENSMUSG00000042677 856 0 3 0 0000000 00 0 0 Zincfinger CCCH type containing 12A 1446786_at 2.238 0.0479 Aplp2 ENSMUSG00000031996 1314 0 0 0 0000001741 5 1 Yes Amyloid beta (A4) precursor-like protein 2, mRNA (cDNA clone IMAGE:4504805) 1422091_at 2.227 0.0441 Pfkfb2 ENSMUSG00000026409 2835 0 3 0 0000004811 0 0 Yes 6-Phosphofructo-2-kinase/fructose-2, 6-biphosphatase 2 1430046_at 2.206 0.0156 Otud3 ENSMUSG00000041161 359 0 0 0 0000000 00 0 0 OTUdomain containing 3 1453739_at 2.193 0.00257 1110001A23Rik ENSMUSG00000030614 784 0 0 0 0000002 00 0 0 RIKENcDNA 1110001A23 gene 1459916_at 2.19 0.045 Pax5 ENSMUSG00000014030 361 0 0 0 0000000 01 0 0 Pairedboxgene 5 (Pax5), mRNA 1418406_at 2.167 0.0132 Pde8a ENSMUSG00000025584 1011 1 4 0 1000015 00 0 0 Phosphodiesterase 8A hc emt netitdnncmeia s,dsrbto n erdcini n eim rvddteoiia oki rprycited. properly is work original the provided medium, any in reproduction and distribution use, non-commerical unrestricted permits which E mice HuD-Tg in genes axogenesis of Expression 01TeAuthor(s) The 2011 Table S1 Continued.

Fold 39 UTR OL Type Type Type Type Type Type Motif Motif Motif Validated Systematic change P-value Gene symbol Ensembl gene ID length ARED AUUUA AUUUA I IIA IIB IIC IID IIE U-rich GRE 1 2 3 target? Gene description

1443484_at 2.164 0.00258 Rpap1 ENSMUSG00000034032 991 0 0 0 0 0 0 0 0 0 0 0 0 0 0 RNA polymerase II associated protein 1 1425476_at 2.145 0.0398 Col4a5 ENSMUSG00000031274 1110 0 3 0 0 0 0 0 0 0 5 0 0 1 0 Collagen, type IV, alpha 5 Gene hsi nOe cesatcedsrbtdudrtetrso h raieCmosAtiuinNnCmeca iec (http://creativecommons.or Licence Non-Commercial Attribution Commons Creative the of terms the under distributed article Access Open an is This 1425842_at 2.136 0.0423 Edil3 ENSMUSG00000034488 3403 1 16 0 0 0 0 0 0 1 43 0 0 1 0 Yes EGF-like repeats and discoidin I-like domains 3 1435804_at 2.136 0.0358 Eif4e2 ENSMUSG00000026254 2676 0 2 0 0 0 0 0 0 0 0 5 1 3 0 Eukaryotic translation initiation factor 4E member 2 1418140_at 2.134 0.0209 Dcx ENSMUSG00000031285 7709 0 13 0 0 0 0 0 0 0 47 0 41 0 0 Doublecortin 1440025_at 2.128 0.0278 Kptn ENSMUSG00000006021 273 0 1 0 0 0 0 0 0 0 0 0 0 0 0 Kaptin 1444786_at 2.123 0.0251 Nol3 ENSMUSG00000014776 2037 0 0 0 0 0 0 0 0 0 0 0 1 0 0 Nucleolar protein 3 (apoptosis repressor with CARD domain) 1450997_at 2.092 0.0388 Stk17b ENSMUSG00000026094 1982 0 6 0 0 0 0 0 0 0 0 0 0 0 0 Serine/threonine kinase 17b (apoptosis-inducing) 1429930_at 2.074 0.0204 Ccdc19 ENSMUSG00000026546 1506 0 1 0 0 0 0 0 0 0 0 0 0 0 0 Coiled-coil domain containing 19 1437171_x_at 2.049 0.00285 Gsn ENSMUSG00000026879 231 0 0 0 0 0 0 0 0 0 9 0 0 1 0 Gelsolin 1455707_at 2.031 0.0139 C130037N17Rik ENSMUSG00000048424 2322 1 10 0 0 0 0 0 0 0 47 2 1 4 1 RIKEN cDNA C130037N17 gene 1443787_x_at 2.031 0.0471 Casp14 ENSMUSG00000005355 1380 0 1 0 0 0 0 0 0 0 0 0 3 0 0 Caspase 14 (Casp14), mRNA 1439887_at 2.027 0.0463 Rnf152 ENSMUSG00000047496 4288 0 17 0 0 0 0 0 0 0 3 1 0 1 2 16 Days embryo head cDNA, RIKEN full-length enriched library, clone:C130025B04 product:ring finger protein 152 1421809_at 2.017 0.0365 Dgcr2 ENSMUSG00000003166 2166 0 1 0 0 0 0 0 0 0 0 0 0 0 0 DiGeorge syndrome critical region gene 2 1450375_at 2.005 0.0285 Pspn ENSMUSG00000002664 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Persephin 1447773_x_at 1.996 0.0419 6330409D20Rik ENSMUSG00000009551 374 0 0 0 0 0 0 0 0 0 1 0 1 1 0 Yes RIKEN cDNA 6330409D20 gene 1437953_at 1.992 0.0352 2310032D16Rik ENSMUSG00000027346 1299 0 2 0 0 0 0 0 0 0 8 0 0 1 0 RIKEN cDNA 2310032D16 gene 1420604_at 1.988 0.0243 Hesx1 ENSMUSG00000040726 202 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Homeo box gene expressed in ES cells 1425895_a_at 1.952 0.0126 Id1 ENSMUSG00000042745 563 0 0 0 0 0 0 0 0 0 0 0 0 0 1 Inhibitor of DNA binding 1 1425838_at 1.94 0.0389 Atp9a ENSMUSG00000027546 334 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ATPase, class II, type 9A 1452352_at 1.933 0.0145 Ctla2b ENSMUSG00000074874 348 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Cytotoxic T lymphocyte-associated protein 2 beta 1439781_at 1.921 0.00321 D930048N14Rik ENSMUSG00000052563 2936 0 1 0 0 0 0 0 0 0 44 11 3 10 0 RIKEN cDNA D930048N14 gene 1447670_at 1.889 0.011 Psmd9 ENSMUSG00000029440 1811 0 2 0 0 0 0 0 0 0 4 0 1 1 1 Proteasome (prosome, macropain) 26S subunit, non-ATPase, 9 1417275_at 1.884 0.0283 Mal ENSMUSG00000027375 1754 0 2 0 0 0 0 0 0 0 0 0 0 0 0 Myelin and lymphocyte protein, T-cell differentiation protein 1430574_at 1.883 0.0246 Cdkn3 ENSMUSG00000037628 137 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Cyclin-dependent kinase inhibitor 3 1418739_at 1.87 0.0305 Sgk2 ENSMUSG00000017868 1053 0 3 0 0 0 0 0 0 0 19 0 0 2 0 Serum/glucocorticoid regulated kinase 2 1439820_at 1.847 0.0313 Ebf1 ENSMUSG00000057098 3343 1 10 0 1 0 0 0 0 1 44 1 2 1 3 Yes Early B-cell factor 1 (Ebf1), mRNA 1418111_at 1.843 0.0488 Tmed11 ENSMUSG00000004821 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Transmembrane emp24 protein transport domain containing Gene 1435701_at 1.832 0.0266 Cyyr1 ENSMUSG00000041134 4657 1 10 0 0 0 0 0 0 0 18 0 54 7 2 Cysteine and tyrosine-rich protein 1 Gene 1422635_at 1.831 0.0408 Ache ENSMUSG00000023328 228 0 2 1 0 0 0 0 0 0 0 0 0 0 0 Yes Acetylcholinesterase 1415677_at 1.829 0.00253 Dhrs1 ENSMUSG00000002332 262 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Dehydrogenase/reductase (SDR family) member 1 1423418_at 1.827 0.0244 Fdps ENSMUSG00000059743 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Farnesyl diphosphate synthetase 1426285_at 1.821 0.0121 Lama2 ENSMUSG00000019899 207 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Laminin, alpha 2 1422146_at 1.813 0.00498 Sema5b ENSMUSG00000052133 986 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B 1431993_a_at 1.804 0.0473 Rnf38 ENSMUSG00000035696 3384 0 6 0 0 0 0 0 0 0 76 2 1 7 2 Yes Ring finger protein 38 1448669_at 1.796 0.0038 Dkk3 ENSMUSG00000030772 2188 0 4 0 0 0 0 0 0 1 3 0 2 0 0 Dickkopf homologue 3 (Xenopus laevis) 1432400_at 1.793 0.041 Epha1 ENSMUSG00000029859 281 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Eph receptor A1 1417081_a_at 1.789 0.0472 Syngr2 ENSMUSG00000048277 808 0 0 0 0 0 0 0 0 0 0 0 1 0 0 Synaptogyrin 2 1447807_s_at 1.783 0.000722 Plekhh1 ENSMUSG00000060716 2053 0 2 0 0 0 0 0 0 0 10 1 1 0 0 Yes Pleckstrin homology domain containing, family H (with MyTH4 domain) member 1 1422839_at 1.781 0.0336 Neurog2 ENSMUSG00000027967 1111 1 7 0 0 0 0 0 0 0 12 0 4 1 0 Neurogenin 2 1434292_at 1.775 0.0361 E130013N09Rik ENSMUSG00000044349 5230 4 11 2 0 0 1 1 2 5 101 0 29 13 2 RIKEN cDNA E130013N09 gene

g/licenses/by-nc/2.5/) 1436991_x_at 1.774 0.0321 Gsn ENSMUSG00000026879 231 0 0 0 0 0 0 0 0 0 9 0 0 1 0 Gelsolin 1450285_at 1.765 0.0328 Ube1y1 ENSMUSG00000071964 702 0 1 0 0 0 0 0 0 0 8 0 0 0 3 Ubiquitin-activating enzyme E1, Chr Y 1 1456174_x_at 1.765 0.012 Ndrg1 ENSMUSG00000005125 1549 0 2 0 0 0 0 0 0 0 0 0 2 0 0 N-myc downstream regulated gene 1 1427523_at 1.764 0.0348 Six3 ENSMUSG00000038805 4096 0 4 0 0 0 0 0 0 0 0 0 0 0 0 Sine oculis-related homeobox 3 homolog (Drosophila) 1446783_at 1.763 0.0352 Rad23a ENSMUSG00000003813 1288 0 3 1 0 0 0 0 0 0 0 0 0 0 0 Yes RAD23a homologue (S. cerevisiae) (Rad23a), mRNA 1427972_at 1.761 0.0287 Cdc73 ENSMUSG00000078284 6500 1 10 1 0 0 0 0 0 0 17 2 1 11 0 Yes Vcell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) 1426176_a_at 1.753 0.0115 Prok2 ENSMUSG00000030069 1003 0 2 0 0 0 0 0 0 0 42 0 0 9 0 Yes Prokineticin 2 1417839_at 1.745 0.0294 Cldn5 ENSMUSG00000041378 608 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Claudin 5 1432230_at 1.741 0.0255 Hip1 ENSMUSG00000039959 6651 0 6 0 0 0 0 0 0 0 0 2 2 1 0 Huntingtin interacting protein 1 1433785_at 1.73 0.0491 Mobp ENSMUSG00000032517 2901 0 2 0 0 0 0 0 0 0 0 0 3 0 0 Myelin-associated oligodendrocytic basic protein 1425850_a_at 1.729 0.0139 Nek6 ENSMUSG00000026749 2651 0 5 0 0 0 0 0 0 0 18 1 0 3 0 NIMA (never in mitosis gene a)-related expressed kinase 6 hc emt netitdnncmeia s,dsrbto n erdcini n eim rvddteoiia oki rprycited. properly is work original the provided medium, any in reproduction and distribution use, non-commerical unrestricted permits which E 01TeAuthor(s) The 2011 Table S1 Continued. ..ProeBzoeoadothers and Perrone-Bizzozero N.I. Fold 39 UTR OL Type Type Type Type Type Type Motif Motif Motif Validated Systematic change P-value Gene symbol Ensembl gene ID length ARED AUUUA AUUUA I IIA IIB IIC IID IIE U-rich GRE 1 2 3 target? Gene description

1416817_at 1.726 0.0213 Nek7 ENSMUSG00000026393 2286 0 4 0 0 0 00003400 5 0 Yes NIMA (never in mitosis gene a)-related

hsi nOe cesatcedsrbtdudrtetrso h raieCmosAtiuinNnCmeca iec (http://creativecommons.or Licence Non-Commercial Attribution Commons Creative the of terms the under distributed article Access Open an is This expressed kinase 7, mRNA (cDNA clone MGC:46827 IMAGE:3994871) 1421594_a_at 1.725 0.0176 Sytl2 ENSMUSG00000030616 891 0 1 0 0 0 00000 00 0 0 Synaptotagmin-like 2 1424012_at 1.719 0.0352 4930506L13Rik ENSMUSG00000075271 1496 0 5 1 0 0 00011400 1 1 RIKENcDNA 4930506L13 gene 1424098_at 1.698 0.00269 Elovl7 ENSMUSG00000021696 1057 0 2 0 0 0 00000 00 0 0 ELOVL family member 7, elongation of long chain fatty acids (yeast) 1445667_at 1.691 0.0499 TBC1D10A ENSMUSG00000034412 352 0 1 0 1 0 00000 00 0 0 TBC1 domain family, member 10a, mRNA (cDNA clone MGC:6862 IMAGE:2650923) 1435642_at 1.689 0.0118 9630019K15Rik ENSMUSG00000055945 2175 0 2 0 0 0 00001 0130 0 RIKENcDNA 9630019K15 gene 1425468_at 1.688 0.0433 Plp1 ENSMUSG00000031425 3622 1 7 0 0 0 00004405 3 3 Yes Proteolipid protein (myelin) 1 1429377_at 1.685 0.0468 2410004A20Rik ENSMUSG00000032214 251 0 1 0 0 0 00000 00 0 0 RIKENcDNA 2410004A20 gene 1424892_at 1.68 0.0256 Zfp95 ENSMUSG00000055991 599 0 0 0 0 0 00000 00 0 0 Zincfinger protein 95 1417600_at 1.666 0.0386 Slc15a2 ENSMUSG00000022899 1597 0 2 0 0 0 00002400 0 0 Yes Solute carrier family 15 (H+/peptide transporter), member 2 1443914_at 1.662 0.0485 Lipl2 ENSMUSG00000024771 782 0 1 0 0 0 00000 00 0 0 Lipase-like, ab-hydrolase domain containing 2, mRNA (cDNA clone MGC:67675 IMAGE:4011597) 1456533_at 1.657 0.0251 Dpy19l1 ENSMUSG00000043067 2491 0 4 0 0 0 00002701 3 3 Yes Dpy-19-like 1 (C. elegans) 1425233_at 1.65 0.0467 2210407C18Rik ENSMUSG00000037145 124 0 0 0 0 0 00000 00 0 0 RIKENcDNA 2210407C18 gene 1457071_x_at 1.648 0.00472 PRMT6 ENSMUSG00000049300 1892 0 4 1 0 0 00000 01 0 0 HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae) 1445727_at 1.648 0.0299 Ube3a ENSMUSG00000025326 1797 1 6 0 0 0 00007000 8 0 Yes Ubiquitin protein ligase E3A 1426600_at 1.644 0.0101 Slc2a1 ENSMUSG00000028645 884 0 1 0 0 0 00002400 1 0 Yes Solute carrier family 2 (facilitated glucose transporter), member 1 1418507_s_at 1.642 0.0137 D130043N08Rik ENSMUSG00000020027 1163 0 2 0 0 0 00002700 1 3 RIKENcDNA D130043N08 gene 1416455_a_at 1.635 0.0381 Cryab ENSMUSG00000032060 135 0 0 0 0 0 00000 00 0 1 Crystallin, alpha B 1426032_at 1.631 0.00791 Nfatc2 ENSMUSG00000027544 288 0 0 0 0 0 00000 00 0 0 Yes Nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 1445186_at 1.616 0.00753 Stc2 ENSMUSG00000020303 2837 0 4 0 0 0 00002912 6 4 Stanniocalcin 2 1436974_at 1.6 0.00152 Tmem88b ENSMUSG00000073680 2677 5 11 2 2 0 01257532 2 1 Transmembrane protein 88b 1418980_a_at 1.6 0.0262 Cnp1 ENSMUSG00000006782 932 0 1 0 0 0 00001401 2 0 Cyclic nucleotide phosphodiesterase 1 1424099_at 1.599 0.0323 2310016C16Rik ENSMUSG00000021760 373 0 0 0 0 0 00000 00 0 0 RIKENcDNA 2310016C16 gene 1448629_at 1.595 0.0463 Hps4 ENSMUSG00000042328 284 0 0 0 0 0 00000 00 0 0 Hermansky-Pudlak syndrome 4 homologue (human) 1424500_at 1.594 0.00979 4732497O03Rik ENSMUSG00000035575 2002 0 3 0 0 0 00001220 0 0 RIKENcDNA 4732497O03 gene 1423754_at 1.589 0.0481 Ifitm3 ENSMUSG00000025492 135 0 1 0 0 0 00000 01 0 0 Interferon induced transmembrane protein 3 1421262_at 1.587 0.00559 Lipg ENSMUSG00000053846 1995 0 5 0 0 0 00001202 1 2 Yes Lipase, endothelial 1452139_at 1.582 0.00466 Slc35c1 ENSMUSG00000049922 1451 0 1 0 0 0 00000 01 0 0 Solutecarrier family 35, member C1 1435254_at 1.581 0.0454 Plxnb1 ENSMUSG00000053646 1967 0 0 0 0 0 00000 00 0 0 PlexinB1 1416003_at 1.576 0.0301 Cldn11 ENSMUSG00000037625 1016 0 1 0 0 0 00001400 0 0 Claudin 11 1433508_at 1.575 0.0103 klf6 ENSMUSG00000000078 3110 0 7 0 0 0 00002001 5 1 Yes Kruppel-like factor 6 (Klf6), mRNA 1416379_at 1.573 0.0409 Panx1 ENSMUSG00000031934 351 0 0 0 0 0 00000 00 0 0 Pannexin 1 1460665_a_at 1.573 0.049 Cnot7 ENSMUSG00000031601 1447 0 5 0 0 0 00002200 0 0 Yes CCR4-NOT transcription complex, subunit 7 1438106_at 1.569 0.0319 Pcdhb22 ENSMUSG00000073591 554 0 0 0 0 0 00000 20 1 1 Protocadherin beta 22 1425065_at 1.561 0.0347 Oas2 ENSMUSG00000032690 1625 0 1 0 0 0 00000 04 0 0 29-59 Oligoadenylate synthetase 2 1420699_at 1.552 0.0345 Clec7a ENSMUSG00000079293 1448 0 1 0 0 0 00000 00 0 0 C-type lectin domain family 7, member a 1426022_a_at 1.546 0.0135 Vill ENSMUSG00000038775 272 0 0 0 0 0 00000 00 0 0 Villin-like 1420760_s_at 1.533 0.0335 Ndrl ENSMUSG00000005125 1546 0 2 0 0 0 00000 02 0 0 N-myc downstream regulated-like 1426529_a_at 1.53 0.0439 Tagln2 ENSMUSG00000026547 672 0 1 0 0 0 00000 0300 0 Transgelin 2 1447841_x_at 1.521 0.0235 ST3GAL6 ENSMUSG00000022747 2522 0 6 0 0 0 00010 01 0 0 ST3beta-galactosidealpha-2,3-sialyltransferase 6, mRNA (cDNA clone IMAGE:1329116) 1420498_a_at 1.518 0.0269 Dab2 ENSMUSG00000022150 1929 0 4 0 0 0 00011904 1 0 Yes Disabled homologue 2 (Drosophila) 1453837_at 1.516 0.0241 6330500D04Rik ENSMUSG00000036006 2131 0 1 0 0 0 00005400 5 0 Yes RIKEN cDNA 6330500D04 gene

g/licenses/by-nc/2.5/) 1440902_at 1.512 0.0191 A330104H05Rik ENSMUSG00000026830 2641 0 11 0 0 0 00000 00 0 0 RIKENcDNA A330104H05 gene 1435795_at 1.505 0.0336 Glb1 ENSMUSG00000045594 480 0 1 0 0 0 00000 01 0 0 Galactosidase, beta 1 1454659_at 1.505 0.0392 Dctd ENSMUSG00000031562 1242 0 2 0 0 0 00001100 0 1 Yes dCMP deaminase 1434537_at 1.503 0.0471 Slco3a1 ENSMUSG00000025790 587 0 0 0 0 0 00000 00 0 0 Solutecarrier organic anion transporter family, member 3a1 1455173_at 1.495 0.0184 Gspt1 ENSMUSG00000062203 4584 0 8 0 0 0 00014 02 0 0 Yes G1 to S phase transition 1 1439236_at 1.493 0.0222 Phf20l1 ENSMUSG00000072501 4683 1 14 0 0 0 00001320 0 2 B16F10Y cells cDNA, RIKEN full-length enriched library, clone:G370109K15 product:PHD finger protein 20-like 1 1453581_at 1.492 0.0245 4933426L22Rik ENSMUSG00000057335 2017 2 9 1 0 0 00129710 4 0 RIKENcDNA 4933426L22 gene 1457585_at 1.488 0.0466 Tmem24 ENSMUSG00000032120 840 2 5 1 2 0 00120 01 0 0 Transmembrane protein 24 1416386_a_at 1.488 0.0151 M6pr ENSMUSG00000007458 1230 0 0 0 0 0 00000 00 0 0 Yes Mannose-6-phosphate receptor, cation dependent 1436010_at 1.487 0.045 BC036313 ENSMUSG00000022211 301 0 0 0 0 0 00000 00 0 0 cDNA sequence BC036313 1450144_at 1.486 0.0394 PLA2R1 ENSMUSG00000054580 3222 0 5 0 0 0 00003 00 1 0 Phospholipase A2, group IB, pancreas, receptor 1432250_at 1.484 0.0455 Utp14a ENSMUSG00000063785 3000 0 0 0 0 0 00002421 4 2 UTP14, U3 small nucleolar ribonucleoprotein, homologue A (yeast) 1434347_s_at 1.482 0.00757 Rufy2 ENSMUSG00000020070 3111 0 6 0 0 0 00008 00 0 0 Transcribed locus, RUN and FYVE domain-containing 2 gene hc emt netitdnncmeia s,dsrbto n erdcini n eim rvddteoiia oki rprycited. properly is work original the provided medium, any in reproduction and distribution use, non-commerical unrestricted permits which E mice HuD-Tg in genes axogenesis of Expression

01TeAuthor(s) The 2011 Table S1 Continued.

1449264_at 1.478 0.0134 Syt11 ENSMUSG00000068923 3000 0 0 0 0 0 00001421 4 2 Yes Synaptotagmin XI 1447634_x_at 1.477 0.0433 Rcbtb2 ENSMUSG00000022106 1619 0 2 0 0 0 00000 01 1 0 Regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing hsi nOe cesatcedsrbtdudrtetrso h raieCmosAtiuinNnCmeca iec (http://creativecommons.or Licence Non-Commercial Attribution Commons Creative the of terms the under distributed article Access Open an is This protein 2 1436201_x_at 1.471 0.0409 Mbp ENSMUSG00000041607 1481 0 1 0 0 0 00000 01 0 0 Yes Myelin basic protein 1434369_a_at 1.471 0.0498 Cryab ENSMUSG00000032060 138 0 0 0 0 0 00000 00 0 1 Crystallin, alpha B 1417693_a_at 1.471 0.00506 Gab1 ENSMUSG00000031714 1889 0 3 0 0 0 00001106 0 0 Growth factor receptor bound protein 2-associated protein 1 1423498_at 1.466 0.014 Aldoa-ps1 ENSMUSG00000063129 510 0 1 0 0 0 00001332 2 0 Aldolase1,Aisoform, pseudogene 1 1450510_a_at 1.466 0.0486 Cacna1a ENSMUSG00000034656 541 0 0 0 0 0 00002400 0 0 Cacna1a mRNA for CaV2.1, complete cds, clone:MPI 1456228_x_at 1.465 0.0314 Mbp ENSMUSG00000041607 3935 0 5 0 0 0 00000 02 0 0 Yes Myelin basic protein 1450258_a_at 1.464 0.0269 Elavl4 ENSMUSG00000028546 2610 1 9 1 0 0 00103100 0 0 Yes ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D) 1423608_at 1.463 0.046 Itm2a ENSMUSG00000031239 792 0 6 0 1 0 00011300 0 0 Integral membrane protein 2A 1434111_at 1.463 0.025 Lphn2 ENSMUSG00000028184 1588 1 3 0 0 0 00011800 3 1 Latrophilin 2 1428927_at 1.461 0.0199 Shq1 ENSMUSG00000035378 183 0 1 0 0 0 00003 00 0 0 SHQ1 homolog (S. cerevisiae) 1457773_at 1.454 0.0178 Slamf6 ENSMUSG00000015314 1276 1 2 0 1 0 00000 02 0 0 SLAM family member 6 1418627_at 1.453 0.00213 Gclm ENSMUSG00000028124 3667 0 5 0 0 0 00009 14 1 2 Glutamate-cysteine ligase, modifier subunit 1425467_a_at 1.45 0.0219 Plp1 ENSMUSG00000031425 3623 1 7 0 0 0 00001705 3 3 Yes Proteolipid protein (myelin) 1 1429078_a_at 1.45 0.0412 Cops7a ENSMUSG00000030127 782 0 1 0 0 0 00000 00 0 0 COP9 (constitutive photomorphogenic) homolog, subunit 7a (Arabidopsis thaliana) 1421105_at 1.45 0.0442 Jag1 ENSMUSG00000027276 1568 4 10 0 2 0 00037401 150 Yes Jagged 1 1438377_x_at 1.449 0.0103 Slc13a3 ENSMUSG00000018459 1652 0 0 0 0 0 00000 01 0 0 Solutecarrier family 13 (sodium-dependent dicarboxylate transporter), member 3 1437341_x_at 1.449 0.0211 Cnp1 ENSMUSG00000006782 932 0 1 0 0 0 00006 01 2 0 Cyclic nucleotide phosphodiesterase 1 1433776_at 1.445 0.0412 Lhfp ENSMUSG00000048332 1070 0 0 0 0 0 00001100 2 0 Lipoma HMGIC fusion partner 1429298_at 1.445 0.0431 Ddah1 ENSMUSG00000028194 2719 0 4 0 0 0 00002801 4 2 Dimethylarginine dimethylaminohydrolase 1 1451782_a_at 1.441 0.0325 Slc29a1 ENSMUSG00000023942 468 0 0 0 0 0 00000 00 0 0 Yes Solute carrier family 29 (nucleoside transporters), member 1 1434098_at 1.441 0.0352 Glra2 ENSMUSG00000018589 1267 0 5 0 0 0 00002 00 0 0 Yes Glycine receptor, alpha 2 subunit 1446560_at 1.439 0.0255 Prss23 ENSMUSG00000039405 1926 0 6 0 0 0 00000 00 0 0 Protease, serine, 23 1448954_at 1.439 0.017 Nrip3 ENSMUSG00000034825 3119 0 4 0 0 0 00003100 1 0 Yes Nuclear receptor interacting protein 3 1416683_at 1.437 0.0169 Plxnb2 ENSMUSG00000036606 732 0 0 0 0 0 00000 01 0 0 PlexinB2 1436547_at 1.437 0.0305 Dgke ENSMUSG00000000276 5553 6 17 2 0 0 00034350 103 YesDiacylglycerol kinase, epsilon 1451260_at 1.435 0.0177 Aldh1b1 ENSMUSG00000035561 581 0 1 0 0 0 00000 00 0 0 Aldehyde dehydrogenase 1 family, member B1 1448830_at 1.435 0.0308 Dusp1 ENSMUSG00000024190 690 1 4 1 0 0 00001020 0 0 Yes Dual specificity phosphatase 1 1446735_at 1.433 0.0373 Itsn2 ENSMUSG00000020640 753 1 1 0 0 0 00000 00 0 0 Intersectin 2 1445253_at 1.431 0.00831 Stx3 ENSMUSG00000041488 1717 0 7 0 0 0 00000 00 0 0 Syntaxin 3 (Stx3), transcript variant C, mRNA 1429141_at 1.429 0.0365 Neurl2 ENSMUSG00000039873 140 0 0 0 0 0 00000 00 0 0 Neuralized-like 2 (Drosophila) 1434256_s_at 1.425 0.0346 Cds2 ENSMUSG00000058793 6765 0 7 0 0 0 00002603 2 0 Yes CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2 1434657_at 1.421 0.00175 Gls ENSMUSG00000026103 2710 0 6 0 0 0 00002500 4 0 Yes MKIAA0838 protein 1436058_at 1.419 0.0102 Rsad2 ENSMUSG00000020641 3613 0 3 0 0 0 00003201 0 0 Yes Radical S-adenosyl methionine domain containing 2 1439904_at 1.417 0.0461 Fstl5 ENSMUSG00000034098 1827 0 7 0 0 0 00011500 0 1 Follistatin-like 5 1435533_s_at 1.415 0.0178 4933426K21Rik ENSMUSG00000040649 3096 0 14 1 0 0 00013971 8 0 RIKENcDNA 4933426K21 gene 1418592_at 1.414 0.0426 Dnaja4 ENSMUSG00000032285 1639 0 2 0 0 0 00000 01 0 0 Yes DnaJ (Hsp40) homologue, subfamily A, member 4 1460249_at 1.414 0.0249 Lnx2 ENSMUSG00000016520 2266 0 3 0 1 0 00003000 1 1 Yes Ligand of numb-protein X 2 1459839_x_at 1.413 0.0191 Btbd11 ENSMUSG00000020042 1943 0 0 0 0 0 00006 01 0 1 BTB(POZ) domain containing 11 1431323_at 1.411 0.0223 Lztfl1 ENSMUSG00000025245 3700 0 15 0 0 0 00000 00 1 0 Yes Leucine zipper transcription factor-like 1 1459838_s_at 1.407 0.00709 Btbd11 ENSMUSG00000020042 1943 0 0 0 0 0 00006 01 0 1 BTB(POZ) domain containing 11 1433501_at 1.404 0.0191 Ctso ENSMUSG00000028015 2465 0 7 0 0 0 00003042 5 0 Cathepsin O 1439647_at 1.398 0.0324 Gm12429 ENSMUSG00000078721 139 0 0 0 0 0 00000 00 0 0 Predicted gene 12429 Pseudogene 1436981_a_at 1.398 0.00676 Ywhaz ENSMUSG00000022285 1948 0 6 0 0 0 00007300 5 2 Yes Tyrosine 3-monooxygenase/tryptophan 5-mono-oxygenase activation protein, zeta g/licenses/by-nc/2.5/) polypeptide 1424523_at 1.397 0.0291 Elmo1 ENSMUSG00000041112 1229 0 1 0 0 0 0000220162 0 Yes Engulfment and cell motility 1, ced-12 homolog (C. elegans) 1437398_a_at 1.397 0.037 Aldh9a1 ENSMUSG00000026687 784 0 1 0 0 0 00000 00 0 0 Aldehyde dehydrogenase 9, subfamily A1 1421851_at 1.394 0.00729 Mtap1b ENSMUSG00000052727 4342 3 13 0 0 0 00001801 151 YesMicrotubule-associated protein 1 B 1448518_at 1.393 0.0414 Timm22 ENSMUSG00000020843 2170 0 2 0 0 0 00008 00 2 1 Translocase of inner mitochondrial membrane 22 homolog (yeast) 1433465_a_at 1.39 0.0146 AI467606 ENSMUSG00000045165 1052 0 1 0 0 0 00001002 0 0 Yes Expressed sequence AI467606 1442226_at 1.378 0.0479 6430702L12 ENSMUSG00000063531 3899 0 8 0 0 0 00014501 3 1 Hypothetical protein 6430702L12 1417201_at 1.376 0.0444 Nt5c2 ENSMUSG00000025041 1987 0 2 0 0 0 00000 00 0 0 59-Nucleotidase, cytosolic II 1439018_at 1.374 0.0454 Fhdc1 ENSMUSG00000041842 824 0 0 0 0 0 00000 00 0 0 FH2domain containing 1 Gene 1423153_x_at 1.374 0.0226 Cfh ENSMUSG00000026365 867 0 3 0 0 0 00000 00 0 0 Complement component factor h 1428835_at 1.373 0.0306 Myh14 ENSMUSG00000030739 407 0 0 0 0 0 00000 00 0 0 Myosin, heavy polypeptide 14 1445634_at 1.373 0.0465 Mapt ENSMUSG00000018411 3903 0 3 0 0 0 00000 15 0 0 Microtubule-associated protein tau, mRNA (cDNA clone MGC:25379 IMAGE:4504850) 1455543_at 1.371 0.012 Klhl18 ENSMUSG00000054792 3632 0 3 0 0 0 00000 11 0 0 Kelch-like 18 (Drosophila) 1429417_at 1.368 0.0471 Chsy3 ENSMUSG00000058152 50 0 0 0 0 0 00000 00 0 0 Yes Chondroitin sulfate synthase 3 Gene Table S1 Continued. hc emt netitdnncmeia s,dsrbto n erdcini n eim rvddteoiia oki rprycited. properly is work original the provided medium, any in reproduction and distribution use, non-commerical unrestricted permits which E 01TeAuthor(s) The 2011 Fold 39 UTR OL Type Type Type Type Type Type Motif Motif Motif Validated Systematic change P-value Gene symbol Ensembl gene ID length ARED AUUUA AUUUA I IIA IIB IIC IID IIE U-rich GRE 1 2 3 target? Gene description ..ProeBzoeoadothers and Perrone-Bizzozero N.I.

1456085_x_at 1.368 0.0329 Cd151 ENSMUSG00000025510 771 0 0 0 0 000000 00 0 0 CD151 antigen 1450693_at 1.368 0.0361 Rgs17 ENSMUSG00000019775 7290 0 27 0 0 000014940 5 1 Regulator of G-protein signaling 17 Gene 1435296_at 1.367 0.00188 Adra2c ENSMUSG00000045318 619 0 0 0 0 000000 00 0 1 Adrenergic receptor, alpha 2c 1416582_a_at 1.366 0.0288 Bad ENSMUSG00000024959 478 0 0 0 0 000000 00 0 0 Bcl-associated death promoter hsi nOe cesatcedsrbtdudrtetrso h raieCmosAtiuinNnCmeca iec (http://creativecommons.or Licence Non-Commercial Attribution Commons Creative the of terms the under distributed article Access Open an is This 1439710_at 1.365 0.0179 Ncoa6ip ENSMUSG00000028233 1614 0 1 0 0 000002710 5 0 Nuclear receptor coactivator 6 interacting protein (Tgs1 homolog) 1456602_at 1.36 0.0395 Tmem231 ENSMUSG00000031951 1914 0 0 0 0 000001502 5 0 Transmembrane protein 231 Gene 1443819_x_at 1.359 0.0414 FIS1 ENSMUSG00000019054 220 0 0 0 0 000000 00 0 0 Tetratricopeptide repeat domain 11 1450117_at 1.358 0.0375 Tcf3 ENSMUSG00000055799 982 0 2 0 0 000001200 0 0 Transcription factor 3 1444874_at 1.358 0.0491 Atp5g1 ENSMUSG00000006057 4252 0 3 0 0 000011411 2 2 YesATPsynthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 1 1422314_at 1.356 0.00698 Clcn6 ENSMUSG00000029016 2522 0 0 0 0 000002 02 0 0 YesChloridechannel 6 1460041_at 1.355 0.0226 Flrt1 ENSMUSG00000047787 3142 0 4 0 0 000000 01 0 0 Fibronectin leucine rich transmembrane protein 1 Gene 1424214_at 1.355 0.0454 9130213B05Rik ENSMUSG00000034981 977 0 2 0 0 000001200 1 0 RIKENcDNA 9130213B05 gene 1452685_at 1.349 0.03 0610009O20Rik ENSMUSG00000024442 748 0 0 0 0 000000 00 0 0 RIKENcDNA 0610009O20 gene 1441178_at 1.348 0.0411 Dtwd2 ENSMUSG00000024505 1516 0 7 0 0 000007820 174 YesDTWdomain containing 2 Gene 1418370_at 1.346 0.039 Tnnc1 ENSMUSG00000021909 174 0 0 0 0 000000 01 0 0 Troponin C, cardiac/slow skeletal 1460070_at 1.343 0.0251 Chst2 ENSMUSG00000033350 3770 0 12 0 0 000003116 173 Carbohydrate sulfotransferase 2 Gene 1423082_at 1.343 0.0412 Derl1 ENSMUSG00000022365 2266 0 2 0 0 000006 01 0 0 Yes Der1-like domain family, member 1 1417492_at 1.342 0.0123 Ctsb ENSMUSG00000021939 3592 1 2 0 0 000000 05 0 0 Cathepsin B 1430274_a_at 1.342 0.0146 Stard3nl ENSMUSG00000003062 468 0 1 0 0 000002100 1 0 Yes STARD3 N-terminal like 1436396_at 1.341 0.0325 D430033N04Rik ENSMUSG00000042050 565 0 2 0 0 000000 00 0 0 RIKENcDNA D430033N04 gene 1450016_at 1.341 0.0473 Ccng1 ENSMUSG00000020326 2316 0 8 0 0 000000 00 0 1 Yes Cyclin G1 1460194_at 1.339 0.036 Phyh ENSMUSG00000026664 370 0 1 0 0 000000 01 0 0 Phytanoyl-CoA hydroxylase 1421571_a_at 1.339 0.0254 Ly6c ENSMUSG00000022584 383 0 1 0 0 000000 00 0 0 Lymphocyte antigen 6 complex, locus C 1428515_at 1.337 0.0395 2410012H22Rik ENSMUSG00000014243 230 0 0 0 0 000000 00 0 0 RIKENcDNA 2410012H22 gene 1460370_at 1.334 0.00455 Top1mt ENSMUSG00000000934 77 0 0 0 0 000000 00 0 0 DNAtopoisomerase 1, mitochondrial 1448101_s_at 1.333 0.0298 Trim27 ENSMUSG00000021326 2099 0 5 0 0 000004320 7 0 Tripartite motif protein 27 1417411_at 1.324 0.0251 Nap1l5 ENSMUSG00000055430 1263 0 4 0 0 000000 00 0 0 Nucleosome assembly protein 1-like 5 1417951_at 1.32 0.0245 Eno3 ENSMUSG00000060600 81 0 0 0 0 000000 00 0 0 Enolase 3, beta muscle 1418293_at 1.32 0.0442 Ifit2 ENSMUSG00000045932 1945 0 3 0 0 000000 00 0 0 Interferon-induced protein with tetratricopeptide repeats 2 1419213_at 1.31 0.0494 Nat6 ENSMUSG00000079334 196 0 0 0 0 000000 00 0 0 N-acetyltransferase 6 1420367_at 1.307 0.0487 Denr ENSMUSG00000023106 1538 0 3 0 0 000001800 5 1 Yes Density-regulated protein 1435561_at 1.303 0.0223 Erf ENSMUSG00000040857 1688 0 1 0 0 000000 03 0 0 Ets2 repressor factor 1447559_at 1.299 0.0191 Gpr25 ENSMUSG00000052759 883 0 0 0 0 000000 0210 0 Gprotein-coupled receptor 25 Gene 1442124_at 1.297 0.0247 AU022252 ENSMUSG00000078584 6500 1 10 1 0 000001221 110 Expressed sequence AU022252 Gene 1441254_at 1.289 0.0397 1810008K04Rik ENSMUSG00000052062 4361 0 5 0 0 000002802 1 0 10dayoldmalepancreas cDNA, RIKEN full-length enriched library, clone:1810008K04 product:hypothetical cysteine-rich region pro- file containing protein, full insert sequence 1456191_x_at 1.287 0.00978 Pacsin3 ENSMUSG00000027257 405 0 0 0 0 000000 00 0 0 Protein kinase C and casein kinase substrate in neurons 3 1419026_at 1.287 0.0463 Daxx ENSMUSG00000002307 114 0 0 0 0 000000 00 0 0 Fasdeath domain-associated protein 1428114_at 1.286 0.00811 Slc14a1 ENSMUSG00000059336 2301 0 7 0 0 000007300 0 0 YesSolutecarrier family 14 (urea transporter), member 1 1456954_at 1.282 0.0186 Kcna6 ENSMUSG00000038077 3499 0 0 0 0 000000 02 0 0 Potassium voltage-gated channel, shaker-related, subfamily, member 6 1456479_at 1.282 0.0184 Snx30 ENSMUSG00000028385 5770 0 6 0 1 000001502 1 0 Sorting nexin family member 30 1438672_at 1.279 0.0169 Parvb ENSMUSG00000022438 2657 0 2 0 0 000003 05 0 0 Parvin,beta (Parvb), mRNA 1440962_at 1.264 0.0481 Slc8a3 ENSMUSG00000079055 1576 0 1 0 0 000000 03 0 0 Solutecarrier family 8 (sodium/calcium exchanger), member 3 1457043_at 1.264 0.0444 Gm1057 ENSMUSG00000051950 2993 0 5 0 0 000000 04 0 0 PREDICTED: similar to beta 3-glycosyltrans- ferase-like [Mus musculus], mRNA sequence 1424699_at 1.264 0.019 4921511K06Rik ENSMUSG00000029769 335 0 0 0 0 000000 00 0 0 RIKENcDNA 4921511K06 gene 1432273_a_at 1.262 0.027 Dfy ENSMUSG00000005338 135 0 0 0 0 000002 00 2 0 Duffy blood group g/licenses/by-nc/2.5/) 1434938_at 1.259 0.00679 Rbm9 ENSMUSG00000033565 1823 0 3 0 0 000007201 8 0 YesRNAbindingmotifprotein 9 1438117_x_at 1.254 0.0428 Tmem41b ENSMUSG00000047554 2595 0 5 0 0 000007 01 0 0 Yes Transmembrane protein 41B 1436603_at 1.252 0.0459 Tbl2 ENSMUSG00000005374 4191 0 4 0 0 000005 03 0 0 Transducin (beta)-like 2 1428490_at 1.238 0.0375 C1galt1 ENSMUSG00000042460 790 0 4 0 1 000010 00 0 0 YesCore1UDP-galactose:N-acetylgalactosamine- alpha-R beta 1,3-galactosyltransferase 1448832_a_at 1.226 0.0161 Cplx1 ENSMUSG00000033615 1575 0 1 0 0 000000 01 0 0 Yes Complexin 1 1434187_at 1.224 0.0431 AI849156 ENSMUSG00000063362 3475 0 6 0 1 000003801 101 Expressed sequence AI849156, mRNA (cDNA clone MGC:67180 IMAGE:6821552) 1421891_at 1.219 0.0205 St3gal2 ENSMUSG00000031749 2205 0 2 0 1 000008 01 1 0 ST3beta-galactoside alpha-2,3-sialyltransferase 2 1428384_at 1.215 0.0297 D4Bwg0951e ENSMUSG00000048706 1691 2 9 0 0 000015020 1 0 YesDNAsegment, Chr 4, Brigham & Women’s Genetics 0951 expressed 1434263_at 1.212 0.048 4930404N11Rik ENSMUSG00000034854 2433 0 0 0 0 000002801 5 2 RIKENcDNA 4930404N11 gene (4930404N11Rik), mRNA 1429561_at 1.196 0.045 Brf2 ENSMUSG00000031487 62 0 1 0 0 000000 00 0 0 BRF2, subunit of RNA polymerase III transcription initiation factor, BRF1-like hc emt netitdnncmeia s,dsrbto n erdcini n eim rvddteoiia oki rprycited. properly is work original the provided medium, any in reproduction and distribution use, non-commerical unrestricted permits which E mice HuD-Tg in genes axogenesis of Expression

01TeAuthor(s) The 2011 Table S1 Continued.

1456155_x_at 1.186 0.024 Fuca1 ENSMUSG00000028673 1097 0 2 0 0 0 00000 02 0 0 Fucosidase, alpha-L- 1, tissue 1436150_at 1.183 0.0471 2310028H24Rik ENSMUSG00000028439 2549 0 2 0 0 0 00004 04 0 1 Adult male testis cDNA, RIKEN full-length enriched library, clone:1700066J24 product: hsi nOe cesatcedsrbtdudrtetrso h raieCmosAtiuinNnCmeca iec (http://creativecommons.or Licence Non-Commercial Attribution Commons Creative the of terms the under distributed article Access Open an is This hypothetical protein, full insert sequence 1455242_at 1.171 0.0497 Foxp1 ENSMUSG00000030067 4752 2 10 1 0 0 001220904 140 YesForkhead box P1 1425364_a_at 1.171 0.0477 Slc3a2 ENSMUSG00000010095 155 0 0 0 0 0 00000 00 0 0 Solutecarrier family 3 (activators of dibasic and neutral amino acid transport), member 2 1436657_at 1.167 0.0499 Gm11744 ENSMUSG00000075410 508 0 0 0 0 0 00000 00 0 0 16days neonate cerebellum cDNA, RIKEN full- length enriched library, clone:9630002G20 product:hypothetical protein, full insert sequence 1429681_a_at 1.167 0.0321 Gpsn2 ENSMUSG00000031708 108 0 0 0 0 0 00000 00 0 0 Glycoprotein, synaptic 2 1453765_at 4.471 0.0306 A330106J01Rik RIKEN cDNA A330106J01 gene 1446792_at 3.86 0.0364 — 15 days embryo male testis cDNA, RIKEN full- length enriched library, clone:8030446M23 product:unclassifiable, full insert sequence 1431149_at 3.753 0.00599 B430105A11Rik RIKEN cDNA B430105A11 gene 1437136_at 3.519 0.0161 5830436I19Rik RIKEN cDNA 5830436I19 gene 1439483_at 3.391 0.0264 AI506816 Expressed sequence AI506816 1446853_at 3.167 0.0387 4930544G21Rik RIKEN cDNA 4930544G21 gene, mRNA (cDNA clone MGC:76468 IMAGE:30431760) 1447975_a_at 3.137 0.0355 LOC545261 Hypothetical protein LOC545261 1447097_at 2.765 0.0211 — — 1432153_at 2.731 0.0133 4933426B08Rik RIKEN cDNA 4933426B08 gene 1459888_at 2.54 0.0126 LOC545261 Hypothetical protein LOC545261 1446177_at 2.485 0.0254 — 10 days neonate skin cDNA, RIKEN full-length enriched library, clone:4732421E14 product:unclassifiable, full insert sequence 1443538_at 2.411 0.0453 — — 1431863_at 2.352 0.0309 4931430N09Rik RIKEN cDNA 4931430N09 gene 1457692_at 2.338 0.0233 2010013E08Rik THAP domain containing, apoptosis associated protein 3, mRNA (cDNA clone MGC:106590 IMAGE:5700290) 1445059_at 2.301 0.0151 C80435 Expressed sequence C80435 1458011_s_at 2.214 0.0274 D4Ertd117e DNA segment, Chr 4, ERATO Doi 117, expressed 1432653_at 2.198 0.0476 1700008H02Rik RIKEN cDNA 1700008H02 gene 1447134_at 2.188 0.0446 2900045N06Rik RIKEN cDNA 2900045N06 gene, mRNA (cDNA clone MGC:90828 IMAGE:30536831) 1445323_at 2.126 0.0128 MGI:2149712 Gene regulated by estrogen in breast cancer protein 1447458_at 2.063 0.0371 9330161A08Rik RIKEN cDNA 9330161A08 gene 1432932_at 2.055 0.0248 — — 1458877_at 2.001 0.0422 — Transcribed locus 1457813_at 1.998 0.0403 1700027N10Rik RIKEN cDNA 1700027N10 gene (1700027N10Rik), mRNA 1439732_at 1.919 0.00429 — 16 days neonate cerebellum cDNA, RIKEN full- length enriched library, clone:9630041I08 product:unclassifiable, full insert sequence 1442299_at 1.904 0.0367 — — 1432849_at 1.868 0.0437 — — 1459642_at 1.86 0.0107 AW046396 Expressed sequence AW046396 (AW046396), mRNA 1442264_at 1.855 0.0242 LOC381240 Similar to calcium and DAG-regulated guanine nucleotide exchange factor I 1432968_at 1.796 0.0461 4930456A14Rik RIKEN cDNA 4930456A14 gene 1458585_at 1.779 0.00498 — Transcribed locus g/licenses/by-nc/2.5/) 1455119_at 1.669 0.0346 C030048B12Rik RIKEN cDNA C030048B12 gene 1458050_at 1.657 0.0245 — — 1444428_at 1.652 0.00368 — — 1454520_at 1.649 0.0353 5830415B17Rik RIKEN cDNA 5830415B17 gene 1439431_x_at 1.63 0.0335 — — 1445411_at 1.576 0.00833 — — 1444854_at 1.569 0.0234 — 16 days neonate male medulla oblongata cDNA, RIKEN full-length enriched library, clone:G630043O09 product:hypothetical protein, full insert sequence 1456197_x_at 1.552 0.0316 — PREDICTED: similar to transmembrane protein SHREW1 [Mus musculus], mRNA sequence 1439597_at 1.542 0.0168 4932417H02Rik Raptor mRNA for p150 target of rapamycin (TOR)-scaffold protein containing WD-repeats 1445682_at 1.497 0.0165 2700099C18Rik RIKEN cDNA 2700099C18 gene 1446820_at 1.473 0.043 6330583I20Rik RIKEN cDNA 6330583I20 gene 1457163_at 1.461 0.00147 D730035F11Rik RIKEN cDNA D730035F11 gene hc emt netitdnncmeia s,dsrbto n erdcini n eim rvddteoiia oki rprycited. properly is work original the provided medium, any in reproduction and distribution use, non-commerical unrestricted permits which E 01TeAuthor(s) The 2011 ..ProeBzoeoadothers and Perrone-Bizzozero N.I. hsi nOe cesatcedsrbtdudrtetrso h raieCmosAtiuinNnCmeca iec (http://creativecommons.or Licence Non-Commercial Attribution Commons Creative the of terms the under distributed article Access Open an is This

Table S1 Continued.

1447507_at 1.438 0.0352 C80406 Expressed sequence C80406 1440185_x_at 1.398 0.000668 — Osteoclast-like cell cDNA, RIKEN full-length enriched library, clone:I420027N08 product: ubiquitin-like 1 (sentrin) activating enzyme E1A, full insert sequence 1436231_at 1.381 0.0262 2900052N01Rik RIKEN cDNA 2900052N01 gene 1441453_at 1.365 0.0475 B930096L08Rik DENN/MADD domain containing 2A (Dennd2a), mRNA 1442421_at 1.35 0.0241 — — 1439771_s_at 1.321 0.0366 LOC236374 Similar to 2-cell-stage, variable group, member 3 1444022_at 1.31 0.0422 — — 1442725_at 1.22 0.0224 — Adult male epididymis cDNA, RIKEN full-length enriched library, clone:9230106H08 product:unclassifiable, full insert sequence 1436401_at 1.187 0.0389 9330128J19Rik RIKEN cDNA 9330128J19 gene 1447246_at 1.162 0.0347 — 0 day neonate thymus cDNA, RIKEN full-length enriched library, clone:A430092C21 product: hypothetical protein, full insert sequence g/licenses/by-nc/2.5/) Expression of axogenesis genes in HuD-Tg mice

Table S2 HuD DGC down-regulated transcripts and associated pathways (a) Transcripts Systematic Fold change P-value Gene symbol Gene title 1454288_at 24.975124378 0.0278 5830468K08Rik RIKEN cDNA 5830468K08 gene 1432698_at 23.623188406 0.00449 2900024I21Rik RIKEN cDNA 2900024I21 gene 1450555_at 22.994011976 0.0192 Tex13 Testis expressed gene 13 1458088_at 22.941176471 0.00708 – – 1458816_at 22.88184438 0.034 – – 1421675_at 22.88184438 0.0394 1700123K08Rik RIKEN cDNA 1700123K08 gene 1459885_s_at 22.865329513 0.000261 Cox7c Cytochrome c oxidase subunit VIIc 1444793_at 22.808988764 0.0149 – – 1460489_at 22.78551532 0.0183 1700097M23Rik RIKEN cDNA 1700097M23 gene 1440433_at 22.673796791 0.0241 Nmt2 N-Myristoyltransferase 2, mRNA (cDNA clone MGC: 46936; IMAGE: 5253732) 1446730_at 22.544529262 0.0337 – – 1459525_at 22.5 0.00438 Cbara1 Calcium binding atopy-related autoantigen 1 (Cbara1), mRNA 1445267_at 22.469135802 0.0373 – – 1456127_at 22.469135802 0.0251 Cnpy1 Canopy 1 homologue (zebrafish) (Source: MGI Symbol;Acc:MGI:2442451) 1429951_at 22.43902439 0.00109 Ssbp2 Single-stranded DNA-binding protein 2 1438333_at 22.34741784 0.019 Prtg Protogenin homologue (Gallus gallus) (Source: MGI Symbol; Acc: MGI:2444710) 1441000_at 22.309468822 0.0411 – Adult male diencephalon cDNA, RIKEN full- length enriched library, clone: 9330129D21 product:unclassifiable, full insert sequence 1449907_at 22.304147465 0.0324 Bcmo1 b-Carotene 15,159-mono-oxygenase 1439040_at 22.283105023 0.0392 Cenpe Centromere protein E 1460136_at 22.272727273 0.0466 – – 1445724_at 22.252252252 0.0492 Iqgap1 IQ motif containing GTPase activating protein 1 (Iqgap1), mRNA 1448076_at 22.247191011 0.0117 Sh2bp1 SH2 domain binding protein 1 (tetratricopeptide repeat containing) (Sh2bp1), mRNA 1459140_at 22.237136465 0.0434 Fam172a Family with sequence similarity 172, member A (Source: MGI Symbol; Acc: MGI:1915925) 1445945_at 22.202643172 0.0449 AU021880 Expressed sequence AU021880 1448112_at 22.164502165 0.000205 Cox7c Cytochrome c oxidase, subunit VIIc 1457653_at 22.155172414 0.021 A630042L21Rik RIKEN cDNA A630042L21 gene, mRNA (cDNA clone IMAGE: 4481800) 1424561_at 22.092050209 0.0225 Ece2 Endothelin converting enzyme 2 1452706_a_at 22.06185567 0.000194 1700027J05Rik RIKEN cDNA 1700027J05 gene 1446589_at 22.057613169 0.0334 4930418P06Rik RIKEN cDNA 4930418P06 gene (4930418P06Rik), mRNA 1437068_at 22.036659878 0.0287 Solt SoxLZ/Sox6 leucine zipper binding protein in testis (Solt), transcript variant 1, mRNA 1430529_at 22.024291498 0.0286 Csnk1a1 Casein kinase 1, a1 1425313_at 21.996007984 0.0359 Carf Calcium response factor 1458975_at 21.976284585 0.00428 – – 1437470_at 21.956947162 0.0191 Pknox1 Pbx/knotted 1 homeobox 1419101_at 21.937984496 0.0398 Sin3a Transcriptional regulator, SIN3A (yeast) 1444851_at 21.926782274 0.0364 Zfp532 Zinc finger protein 532, mRNA (cDNA clone MGC:102230; IMAGE: 30618961) 1442263_at 21.919385797 0.0168 Rgs13 Regulator of G-protein signaling 13 1419362_at 21.912045889 0.0193 Mrpl35 Mitochondrial ribosomal protein L35 1436865_at 21.908396947 0.0218 Slc26a11 Solute carrier family 26, member 11 1429981_a_at 21.904761905 0.0232 4933426K21Rik RIKEN cDNA 4933426K21 gene 1440761_at 21.883239171 0.0247 Ssbp2 Single-stranded DNA-binding protein 2 1446738_at 21.858736059 0.0124 – 16 days embryo head cDNA, RIKEN full- length enriched library, clone:C130085H20 product:unclassifiable, full insert sequence 1416602_a_at 21.858736059 0.0311 Rad52 RAD52 homologue (S. cerevisiae) 1451547_at 21.851851852 0.0085 0610009A07Rik RIKEN cDNA 0610009A07 gene 1448786_at 21.801801802 0.016 Plbd1 Phospholipase B domain containing 1 (Source: MGI Symbol; Acc: MGI:1914107) 1418743_a_at 21.798561151 0.00917 MGI:1930803 Tescalcin 1433191_at 21.795332136 0.0294 A430105P17Rik RIKEN cDNA A430105P17 gene 1425598_a_at 21.795332136 0.0491 Lyn Yamaguchi sarcoma viral (v-yes-1) oncogene homologue 1435292_at 21.795332136 0.0411 Tbc1d4 TBC1 domain family, member 4 1440742_at 21.792114695 0.0108 Epc1 Enhancer of polycomb homologue 1 (Drosophila) (Epc1), transcript variant 1, mRNA 1428757_at 21.779359431 0.0259 Aasdhppt Aminoadipate-semialdehyde dehydrogenase- phosphopantetheinyl transferase 1428266_at 21.776198934 0.0359 Myl3 Myosin, light polypeptide 3 1457921_at 21.766784452 0.0441 1810037C20Rik RIKEN cDNA 1810037C20 gene

E 2011 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial Licence (http://creativecommons.org/licenses/by-nc/2.5/) which permits unrestricted non-commerical use, distribution and reproduction in any medium, provided the original work is properly cited. N.I. Perrone-Bizzozero and others

Table S2 Continued.

Systematic Fold change P-value Gene symbol Gene title 1459347_at 21.76056338 0.0323 Gm11190 Predicted gene 11190 (Source: MGI Symbol; Acc: MGI:3651694) 1431965_at 21.739130435 0.00879 4933411E08Rik RIKEN cDNA 4933411E08 gene 1458073_at 21.733102253 0.0315 9330156P08Rik RIKEN cDNA 9330156P08 gene 1459388_at 21.730103806 0.0199 – – 1426850_a_at 21.727115717 0.00699 Map2k6 Mitogen-activated protein kinase kinase 6 1431566_at 21.718213058 0.00584 9030622O22Rik RIKEN cDNA 9030622O22 gene (Source: MGI Symbol; Acc: MGI:1918820) 1418920_at 21.709401709 0.0172 Cldn15 Claudin 15 1457062_at 21.697792869 0.03 1700081L11Rik 1443531_at 21.692047377 0.0194 A930005I04Rik RIKEN cDNA A930005I04 gene 1451732_at 21.686340641 0.0464 Prpf4b PRP4 pre-mRNA processing factor 4 homologue B (yeast) 1448011_at 21.683501684 0.0227 Vps13c Predicted: Mus musculus vacuolar protein sorting 13C (yeast) (Vps13c), mRNA 1430869_a_at 21.683501684 0.0182 Habp4 Hyaluronic acid binding protein 4 1443437_at 21.680672269 0.015 – Predicted: similar to hypothetical protein MGC27016 (Mus musculus), mRNA sequence 1455878_at 21.677852349 0.0154 2700023E23Rik RIKEN cDNA 2700023E23 gene 1446484_at 21.672240803 0.00395 Mef2c Myocyte enhancer factor 2C, mRNA (cDNA clone MGC: 46981; IMAGE: 4500786) 1453522_at 21.661129568 0.0445 6530401N04Rik RIKEN cDNA 6530401N04 gene 1420141_at 21.661129568 0.00395 AA517023 Expressed sequence AA517023 1457497_at 21.658374793 0.0176 – – 1418636_at 21.655629139 0.00411 Etv3 Ets variant gene 3 1453457_at 21.655629139 0.0443 2900070H08Rik RIKEN cDNA 2900070H08 gene 1442710_at 21.652892562 0.00511 Pdlim5 PDZ and LIM domain 5, mRNA (cDNA clone MGC: 46824; IMAGE: 4457868) 1435147_x_at 21.652892562 0.0271 Igsf4d Immunoglobulin superfamily, member 4 1460615_at 21.650165017 0.00919 Nt5c2l1 59-Nucleotidase, cytosolic II-like 1 1437645_at 21.644736842 0.0448 Atf7 Activating transcription factor 7 1450045_at 21.644736842 0.00698 Srrm1 Serine/arginine repetitive matrix 1 1442432_x_at 21.633986928 0.0268 Atxn7l1 Ataxin 7-like 1 1430412_at 21.628664495 0.0294 2310068C19Rik RIKEN cDNA 2310068C19 gene 1438550_x_at 21.62601626 0.0471 Srr Serine racemase 1442042_at 21.620745543 0.0359 – – 1431946_a_at 21.620745543 0.0142 Apba2bp Amyloid b (A4) precursor protein-binding, family A, member 1 binding protein 1459603_at 21.618122977 0.0116 C330008K14Rik RIKEN cDNA C330008K14 gene 1443702_at 21.615508885 0.00999 Mtap4 Microtubule-associated protein 4 1458483_at 21.612903226 0.0389 A330102I10Rik RIKEN cDNA A330102I10 gene 1442626_at 21.612903226 0.0321 5730405I09Rik RIKEN cDNA 5730405I09 gene, mRNA (cDNA clone MGC: 28252; IMAGE: 3995040) 1444980_at 21.612903226 0.00373 – Adult male liver tumor cDNA, RIKEN full- length enriched library, clone: C730009D12 product: unclassifiable, full insert sequence 1457347_at 21.612903226 0.0136 Ryr1 Ryanodine receptor 1, skeletal muscle 1434902_at 21.610305958 0.0434 Rnf157 Ring finger protein 157 1434226_at 21.607717042 0.0375 Cyb561d1 Cytochrome b-561 domain containing 1 1445201_at 21.597444089 0.00736 Zfp53 Zinc finger protein 53 1436385_at 21.594896332 0.0131 Ganc Glucosidase, a; neutral C 1431687_at 21.577287066 0.0214 Gmfb Glia maturation factor, b 1441132_at 21.572327044 0.0113 Hnrpab Heterogeneous nuclear ribonucleoprotein A/ B (Hnrpab), mRNA 1447408_at 21.572327044 0.0141 4933421G18Rik Nipped-B homologue (Drosophila) (Nipbl), transcript variant B, mRNA 1426951_at 21.569858713 0.0315 Crim1 Cysteine-rich transmembrane BMP regulator 1 (chordin like) 1435366_at 21.567398119 0.0189 D430042O09Rik RIKEN cDNA D430042O09 gene 1424526_a_at 21.564945227 0.0137 Tgds TDP-glucose 4,6-dehydratase 1438591_at 21.5625 0.0284 2610019A05Rik RIKEN cDNA 2610019A05 gene 1451977_at 21.5625 0.0166 Dyrk1a Dual-specificity tyrosine-(Y)-phosphoryla- tion regulated kinase 1a 1424989_at 21.557632399 0.00108 D730049H07Rik RIKEN cDNA D730049H07 gene 1447091_at 21.555209953 0.00632 Jmjd2c Jumonji domain containing 2C (Jmjd2c), mRNA 1459590_at 21.550387597 0.0219 1500005P14Rik RIKEN cDNA 1500005P14 gene, mRNA (cDNA clone IMAGE: 5709951) 1440584_at 21.547987616 0.0482 9130221L21Rik RIKEN cDNA 9130221L21 gene 1419216_at 21.545595054 0.028 Azi1 5-Azacytidine induced gene 1 1424116_x_at 21.540832049 0.00721 Ppp5c Protein phosphatase 5, catalytic subunit 1442254_at 21.53609831 0.0074 – Transcribed locus 1444101_at 21.53609831 0.0128 Odf2 Outer dense fibre of sperm tails 2 (Odf2), mRNA 1435090_at 21.526717557 0.0318 Tubgcp6 Tubulin, c complex associated protein 6

Table S2 Continued.

Systematic Fold change P-value Gene symbol Gene title 1438871_at 21.526717557 0.0487 Son Son cell proliferation protein (Son), transcript variant 2, mRNA 1458147_at 21.526717557 0.00809 – – 1432724_at 21.524390244 0.023 4930445G23Rik RIKEN cDNA 4930445G23 gene 1440508_at 21.522070015 0.0416 – – 1440068_at 21.519756839 0.0459 – – 1449431_at 21.519756839 0.00703 Trpc6 Transient receptor potential cation channel, subfamily C, member 6 1447023_at 21.510574018 0.00962 – – 1459956_at 21.510574018 0.0208 Dock10 MKIAA0694 protein 1457690_at 21.506024096 0.0192 Kalrn Kalirin, RhoGEF kinase 1443180_at 21.501501502 0.0349 Mlstd1 Male sterility domain containing 1, mRNA (cDNA clone MGC: 67167; IMAGE: 6809131) 1460031_at 21.494768311 0.032 Gpr45 G-protein-coupled receptor 45 1436902_x_at 21.494768311 0.0438 Tmsb10 Thymosin, b10 1455966_s_at 21.492537313 0.0135 Nudt21 Nudix (nucleoside diphosphate linked moiety X)-type motif 21 1443276_at 21.492537313 0.0205 Htr5a 5-Hydroxytryptamine (serotonin) receptor 5A 1444835_at 21.490312966 0.0223 BC030499 cDNA sequence BC030499 1458074_at 21.488095238 0.00513 – – 1459632_at 21.483679525 0.0361 Crim1 Cysteine-rich repeat-containing protein CRIM1 (Crim1) 1426560_a_at 21.479289941 0.0308 Npnt Nephronectin 1459782_x_at 21.474926254 0.0465 Abcc5 ATP-binding cassette, sub-family C (CFTR/ MRP), member 5 1440042_at 21.47275405 0.0199 Ank2 Ankyrin 2, brain 1435529_at 21.47275405 0.0437 Ifit3 Interferon-induced protein with tetratricopeptide repeats 3, mRNA (cDNA clone MGC: 6081; IMAGE: 3487345) 1453429_at 21.47275405 0.00387 9530057J20Rik RIKEN cDNA 9530057J20 gene 1450050_at 21.470588235 0.0258 Hira Histone cell cycle regulation defective homologue A (S. cerevisiae) 1459246_at 21.470588235 0.0162 D230021J17Rik RIKEN cDNA D230021J17 gene 1421113_at 21.468428781 0.00837 Pga5 Pepsinogen 5, group I 1431084_x_at 21.464128843 0.0352 1810014B01Rik RIKEN cDNA 1810014B01 gene 1438558_x_at 21.457725948 0.0233 Foxq1 Forkhead box Q1 (Foxq1), mRNA 1420401_a_at 21.455604076 0.00703 Ramp3 Receptor (calcitonin) activity modifying protein 3 1457228_x_at 21.453488372 0.03 Gle1l GLE1 RNA export mediator-like (yeast 1448151_at 21.45137881 0.0064 Elavl1 ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R) 1456238_at 21.45137881 0.0173 – Adult male urinary bladder cDNA, RIKEN full- length enriched library, clone: 9530016A12; product: hypothetical protein, full insert sequence 1432024_at 21.445086705 0.0325 2310015L07Rik RIKEN cDNA 2310015L07 gene 1434849_at 21.445086705 0.0219 Tspyl2 TSPY-like 2 1430752_at 21.445086705 0.0197 C330006D17Rik RIKEN cDNA C330006D17 gene 1459453_at 21.443001443 0.0299 Robo1 Dutt1 protein 1435279_at 21.443001443 0.00218 BC059842 cDNA sequence BC059842 1439565_at 21.438848921 0.0305 – CDNA clone IMAGE: 6402034 1453848_s_at 21.436781609 0.04 Zbed3 Zinc finger, BED domain containing 3 1451218_at 21.43472023 0.00322 Edem1 ER degradation enhancer, mannosidase a-like 1 1447962_at 21.43472023 0.026 – Transcribed locus 1436697_at 21.43472023 0.00858 Dscr3 Down syndrome critical region gene 3, mRNA (cDNA clone MGC:5833 IMAGE: 3592608) 1418585_at 21.432664756 0.0206 Ccnh Cyclin H 1440254_at 21.432664756 0.0298 – Transcribed locus 1436634_at 21.430615165 0.00198 Robo3 Roundabout homologue 3 (Drosophila) 1458397_at 21.428571429 0.0492 Dnaja1 DnaJ (Hsp40) homologue, subfamily A, member 1 (Dnaja1), mRNA 1445415_at 21.426533524 0.0307 Inhba Inhibin b-A (Inhba), mRNA 1454808_at 21.426533524 0.0371 Efha1 EF hand domain family A1 1441370_at 21.424501425 0.0256 3632431M01Rik Transmembrane and coiled coil domains 1, mRNA (cDNA clone IMAGE: 3968813) 1443929_at 21.422475107 0.0322 – – 1430662_at 21.422475107 0.0258 9430091E24Rik RIKEN cDNA 9430091E24 gene 1424007_at 21.422475107 0.0363 Gdf10 Growth differentiation factor 10 1417300_at 21.420454545 0.0497 Smpdl3b Sphingomyelin phosphodiesterase, acid-like 3B 1436600_at 21.420454545 0.0236 Tnrc9 Trinucleotide repeat containing 9 1452312_at 21.420454545 0.00315 2810002D19Rik RIKEN cDNA 2810002D19 gene 1416805_at 21.416430595 0.0331 1110032E23Rik RIKEN cDNA 1110032E23 gene 1440485_at 21.416430595 0.0418 – –

Table S2 Continued.

Systematic Fold change P-value Gene symbol Gene title 1446508_at 21.414427157 0.0372 – 13 Days embryo male testis cDNA, RIKEN full-length enriched library, clone: 6030447N08; product: unclassifiable, full insert sequence 1434943_at 21.414427157 0.0402 BC023055 cDNA sequence BC023055 1428106_at 21.410437236 0.017 1300001I01Rik RIKEN cDNA 1300001I01 gene 1454703_x_at 21.410437236 0.0318 Rnu22 RNA, U22 small nucleolar 1430311_at 21.406469761 0.0401 Marcks Myristoylated alanine rich protein kinase C substrate (Marcks), mRNA 1450319_at 21.406469761 0.044 Gabrb2 c-Aminobutyric acid (GABA-A) receptor, subunit b2 1457211_at 21.406469761 0.0284 Gls MKIAA0838 protein 1431071_at 21.404494382 0.00888 Mtx3 Metaxin 3 1425774_at 21.400560224 0.023 1500001A10Rik RIKEN cDNA 1500001A10 gene 1434488_at 21.400560224 0.016 Arfrp1 ADP-ribosylation factor related protein 1 1456355_s_at 21.398601399 0.016 Srr1 Sensitivity to red light reduced homologue (Arabidopsis) 1439126_at 21.396648045 0.0495 Inpp5f Inositol polyphosphate-5-phosphatase F, mRNA (cDNA clone IMAGE: 6816706) 1427795_s_at 21.396648045 0.02 – Mus musculus, clone IMAGE: 5068294 1442813_at 21.396648045 0.0284 C130010K08Rik PREDICTED: RIKEN cDNA C130010K08 gene (Mus musculus), mRNA sequence 1440050_at 21.394700139 0.031 Hbs1l Hbs1-like (S. cerevisiae) 1420500_at 21.39275766 0.0285 Dnajc1 DnaJ (Hsp40) homologue, subfamily C, member 1 1428368_at 21.390820584 0.0181 Arhgap21 Rho GTPase activating protein 21 1444421_at 21.386962552 0.0343 Etohd2 Ethanol decreased 2 1418901_at 21.386962552 0.0458 Cebpb CCAAT/enhancer binding protein (C/EBP), b 1440051_at 21.386962552 0.0206 Ppp3ca Protein phosphatase 3, catalytic subunit, a isoform (Ppp3ca), mRNA 1437184_at 21.385041551 0.044 AA407526 Expressed sequence AA407526 1437339_s_at 21.385041551 0.0328 Pcsk5 Proprotein convertase subtilisin/kexin type 5 1446228_at 21.385041551 0.0319 D19Wsu12e DNA segment, Chr 19, Wayne State University 12, expressed 1456724_x_at 21.383125864 0.0363 Wdr79 WD repeat domain 79 1437273_at 21.383125864 0.00975 Htra4 HtrA serine peptidase 4 1455219_at 21.383125864 0.0237 1110030E23Rik RIKEN cDNA 1110030E23 gene 1455212_at 21.377410468 0.0177 Wdr24 WD repeat domain 24 1450955_s_at 21.373626374 0.0278 Sort1 Sortilin 1 1451520_at 21.373626374 0.00189 – – 1434462_at 21.371742112 0.0343 BC088983 cDNA sequence BC088983 1449980_a_at 21.369863014 0.0231 Gabrd c-Aminobutyric acid (GABA-A) receptor, subunit delta 1434736_at 21.36425648 0.012 Hlf Hepatic leukaemia factor 1423370_a_at 21.36239782 0.0245 Csnk1g2 Casein kinase 1, c2 1441164_at 21.360544218 0.033 4933432P15Rik MKIAA0621 protein 1441369_at 21.360544218 0.0199 C030017B01Rik RIKEN cDNA C030017B01 gene 1440364_a_at 21.358695652 0.0181 A230062G08Rik RIKEN cDNA A230062G08 gene 1420372_at 21.358695652 0.0343 Sntb2 Syntrophin, basic 2 1424137_at 21.358695652 0.0367 Gprin1 G-protein-regulated inducer of neurite outgrowth 1 1427254_at 21.358695652 0.0399 Zfp445 Zinc finger protein 445 1437129_at 21.358695652 0.0282 E330018D03Rik RIKEN cDNA E330018D03 gene 1423049_a_at 21.356852103 0.0138 Tpm1 Tropomyosin 1, a 1426477_at 21.35501355 0.0311 Rasa1 RAS p21 protein activator 1 1438282_at 21.35501355 0.00616 Syt1 Synaptotagmin I 1416254_a_at 21.351351351 0.0432 Vps16 Vacuolar protein sorting 16 (yeast) 1460333_at 21.349527665 0.0342 Ddx59 DEAD (Asp-Glu-Ala-Asp) box polypeptide 59 1419190_at 21.347708895 0.042 Vti1a Vesicle transport through interaction with t-SNAREs homologue 1A (yeast) 1419838_s_at 21.347708895 0.0495 Plk4 Polo-like kinase 4 (Drosophila) 1423577_at 21.347708895 0.0137 Ankrd32 Ankyrin repeat domain 32 1428301_at 21.347708895 0.0406 LOC544986 /// Similar to hypothetical protein LOC67055 /// LOC544988 /// hypothetical protein LOC544988 /// similar LOC544991 /// to hypothetical protein LOC67055 /// hypo- LOC545001 /// thetical protein LOC545001 /// hypothetical LOC545005 /// protein LOC545005 /// hypothetical protein LOC545007 /// LOC545007 /// RIKEN cDNA 2610042L04 2610042L04Rik /// gene /// similar to hypothetical protein LOC545017 LOC67055 1418200_at 21.342281879 0.0209 Hkr3 GLI-Kruppel family member HKR3 1426046_a_at 21.342281879 0.00931 Rabggta Rab geranylgeranyl transferase, a-subunit 1458135_at 21.342281879 0.0114 – – 1423894_a_at 21.340482574 0.0409 Dalrd3 DALR anticodon binding domain containing 3

Table S2 Continued.

Systematic Fold change P-value Gene symbol Gene title 1416532_at 21.340482574 0.00985 Trrap Transformation/transcription domain- associated protein 1436056_at 21.340482574 0.019 Kif13b Kinesin family member 13B 1423056_at 21.336898396 0.0174 Nsg1 Neuron specific gene family member 1 1427212_at 21.333333333 0.0498 Mapkap1 Mitogen-activated protein kinase associated protein 1 1419093_at 21.331557923 0.0268 Tdo2 Tryptophan 2,3-dioxygenase 1451506_at 21.329787234 0.0441 Mef2c Myocyte enhancer factor 2C 1426422_at 21.328021248 0.00469 Cc2d1a Coiled-coil and C2 domain containing 1A 1452397_at 21.326259947 0.00799 2810474O19Rik RIKEN cDNA 2810474O19 gene 1450090_at 21.324503311 0.0216 Zfp101 Zinc finger protein 101 1424270_at 21.324503311 0.0208 Dcamkl1 Double cortin and calcium/calmodulin- dependent protein kinase-like 1 1424557_at 21.324503311 0.035 Zcchc9 Zinc finger, CCHC domain containing 9 1451576_at 21.324503311 0.0382 Prkdc Protein kinase, DNA activated, catalytic polypeptide 1455086_at 21.322751323 0.0366 Uchl5 Ubiquitin C-terminal esterase L5, mRNA (cDNA clone MGC:6295 IMAGE: 2650799) 1444845_at 21.321003963 0.0444 Scfd1 Sec1 family domain containing 1, mRNA (cDNA clone MGC: 38021; IMAGE: 5151118) 1429042_at 21.319261214 0.0357 2010200O16Rik RIKEN cDNA 2010200O16 gene 1434611_at 21.319261214 0.0269 Rnf123 Ring finger protein 123 1453141_at 21.319261214 0.0287 0610009L18Rik RIKEN cDNA 0610009L18 gene 1429703_at 21.315789474 0.0366 2900072G11Rik RIKEN cDNA 2900072G11 gene 1450034_at 21.314060447 0.0155 Stat1 Signal transducer and activator of transcription 1 1432195_s_at 21.312335958 0.00567 Ccnl2 Cyclin L2 1441155_at 21.312335958 0.0323 – – 1428195_at 21.31061599 0.00742 4631427C17Rik RIKEN cDNA 4631427C17 gene 1431359_a_at 21.308900524 0.0185 1110007C09Rik RIKEN cDNA 1110007C09 gene 1455461_at 21.308900524 0.00998 A530017D24Rik RIKEN cDNA A530017D24 gene 1435353_a_at 21.307189542 0.021 4933439C20Rik RIKEN cDNA 4933439C20 gene 1458697_at 21.307189542 0.0154 – Transcribed locus 1448175_at 21.305483029 0.0432 Ehd1 EH-domain containing 1 1416597_at 21.302083333 0.0237 Hdgfrp2 Hepatoma-derived growth factor, related protein 2 1423969_at 21.300390117 0.0131 Nup37 Nucleoporin 37 1428244_at 21.300390117 0.0319 Larp1 La ribonucleoprotein domain family, member 1 1429335_at 21.300390117 0.0432 Snapc1 Small nuclear RNA activating complex, polypeptide 1 1447156_at 21.300390117 0.0245 Chm Choroidermia (Chm), mRNA 1452797_at 21.298701299 0.042 2310010B21Rik RIKEN cDNA 2310010B21 gene 1451339_at 21.295336788 0.0301 Suox Sulfite oxidase 1426986_at 21.293661061 0.0385 2810485I05Rik RIKEN cDNA 2810485I05 gene 1422758_at 21.293661061 0.0411 Chst2 Carbohydrate sulfotransferase 2 1452738_at 21.293661061 0.0135 Stoml1 Stomatin-like 1 1419247_at 21.293661061 0.0061 Rgs2 Regulator of G-protein signaling 2 1422299_a_at 21.290322581 0.0484 Styxl1 Serine/threonine/tyrosine interacting-like 1 1418187_at 21.288659794 0.0428 Ramp2 Receptor (calcitonin) activity modifying protein 2 1436479_a_at 21.288659794 0.0248 Dpp7 Dipeptidylpeptidase 7 1446366_at 21.287001287 0.0379 Trpc4 Transient receptor potential cation channel, subfamily C, member 4 1452780_at 21.287001287 0.0142 Gtf3c2 General transcription factor IIIC, polypeptide 2, b 1436081_a_at 21.283697047 0.0189 Zfp414 Zinc finger protein 414 1417432_a_at 21.282051282 0.0109 Gnb1 Guanine nucleotide binding protein, b1 1437568_at 21.282051282 0.0477 Mmp16 Matrix metallopeptidase 16 1440030_at 21.282051282 0.0219 E330038N15Rik PREDICTED: similar to sodium-and chloride- activated ATP-sensitive potassium channel (SLICK). (Mus musculus), mRNA sequence 1416340_a_at 21.280409731 0.0458 Man2b1 Mannosidase 2, aB1 1428691_at 21.280409731 0.0303 5630401D06Rik RIKEN cDNA 5630401D06 gene 1455675_a_at 21.280409731 0.0321 Tial1 Tial1 cytotoxic granule-associated RNA-binding protein-like 1 1446264_at 21.278772379 0.00221 – – 1436525_at 21.278772379 0.0456 Ap3s2 Adaptor-related protein complex 3, sigma 2 subunit 1442660_at 21.277139208 0.032 Ppil2 Peptidylprolyl isomerase (cyclophilin)-like 2, mRNA (cDNA clone MGC: 19011; IMAGE: 4021590) 1433758_at 21.275510204 0.0308 Nisch Nischarin 1453183_at 21.27388535 0.00685 1110034A24Rik RIKEN cDNA 1110034A24 gene 1433843_at 21.272264631 0.0418 Hs1bp3 HS1-binding protein 3 (Hs1bp3), mRNA

Table S2 Continued.

Systematic Fold change P-value Gene symbol Gene title 1425419_a_at 21.267427123 0.0279 Raf1 v-raf-1 leukemia viral oncogene 1 1452094_at 21.267427123 0.0318 P4ha1 procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), a1 polypeptide 1439571_at 21.265822785 0.0283 E230008J23Rik RIKEN cDNA E230008J23 gene 1432719_at 21.262626263 0.00994 4833412K13Rik RIKEN cDNA 4833412K13 gene 1434031_at 21.261034048 0.0000858 Zfp692 Zinc finger protein 692 1427535_s_at 21.259445844 0.0358 AW822216 Expressed sequence AW822216 1418605_at 21.256281407 0.015 Nr2c1 Nuclear receptor subfamily 2, group C, member 1 1438665_at 21.256281407 0.0351 Smpd3 Sphingomyelin phosphodiesterase 3, neutral 1438419_at 21.253132832 0.0421 Rbm16 RNA-binding motif protein 16 1436078_at 21.251564456 0.0351 Fcho1 FCH domain only 1 1457673_at 21.251564456 0.0487 2610005L07Rik RIKEN cDNA 2610005L07 gene 1453169_a_at 21.243781095 0.0393 Gtf2h1 General transcription factor II H, polypeptide 1 1420140_at 21.239157373 0.0422 Bcdin3 bin3, bicoid-interacting 3, homologue (Drosophila) 1428795_at 21.237623762 0.0463 1110021L09Rik RIKEN cDNA 1110021L09 gene 1448488_at 21.237623762 0.0435 Mrps5 Mitochondrial ribosomal protein S5 1417468_at 21.236093943 0.0446 Nit1 Nitrilase 1 1420481_at 21.236093943 0.0315 – – 1433682_at 21.236093943 0.0178 Arhgef17 Rho guanine nucleotide exchange factor (GEF) 17 1437720_at 21.236093943 0.0335 Lgtn Ligatin, mRNA (cDNA clone MGC: 36900; IMAGE: 4935223) 1433757_a_at 21.234567901 0.0387 Nisch Nischarin 1434901_at 21.234567901 0.0351 Gm1103 /// LOC544682 Gene model 1103, (NCBI) /// ZBTB2-like 1416925_at 21.233045623 0.0368 Kpnb1 Karyopherin (importin) b1 1428494_a_at 21.233045623 0.0497 Polr2i Polymerase (RNA) II (DNA directed) polypeptide I 1419290_at 21.2300123 0.0426 1600013P15Rik RIKEN cDNA 1600013P15 gene 1430769_s_at 21.226993865 0.0314 2900009I07Rik RIKEN cDNA 2900009I07 gene 1443033_at 21.225490196 0.0269 Rbm14 RNA-binding motif protein 14 1448278_at 21.225490196 0.0351 Xab2 XPA-binding protein 2 1415904_at 21.223990208 0.0296 Lpl Lipoprotein lipase 1455178_at 21.223990208 0.0128 Rutbc1 RUN and TBC1 domain containing 1 1455904_at 21.222493888 0.0457 Gas5 Growth arrest specific 5 1435685_x_at 21.219512195 0.0398 Abcc5 ATP-binding cassette, sub-family C (CFTR/MRP), member 5 1437676_at 21.216545012 0.0129 Spag9 Sperm-associated antigen 9 1437563_at 21.215066829 0.0141 – – 1423031_at 21.213592233 0.0296 – – 1452920_a_at 21.209189843 0.0344 Ppil2 Peptidylprolyl isomerase (cyclophilin)-like 2 1434179_at 21.206272618 0.0452 Mll3 Myeloid/lymphoid or mixed-lineage leukemia 3 1441253_at 21.203369434 0.0431 Rfx3 Regulatory factor X, 3 (influences HLA class II expression), mRNA (cDNA clone MGC: 27565; IMAGE: 4483833) 1434270_at 21.200480192 0.0236 Nptxr Neuronal pentraxin receptor 1455143_at 21.200480192 0.00883 Nlgn2 Neuroligin 2 1435177_a_at 21.199040767 0.0176 Anapc5 Anaphase-promoting complex subunit 5 1416924_at 21.193317422 0.0267 Bri3 Brain protein I3 1440376_at 21.191895113 0.0482 Fbxo41 PREDICTED: Mus musculus F-box protein 41 (Fbxo41), mRNA 1433909_at 21.189060642 0.019 Syt17 Synaptotagmin XVII 1455273_at 21.189060642 0.0329 Zfp482 Zinc finger protein 482 (Zfp482), mRNA 1440106_at 21.176470588 0.0353 Tcf4 Transcription factor 4, mRNA (cDNA clone MGC: 13998; IMAGE: 4014231) 1423558_at 21.175088132 0.0408 Ifngr2 Interferon c receptor 2 1457389_at 21.165501166 0.0482 9830166K06Rik RIKEN cDNA 9830166K06 gene (b) Pathways Ingenuity canonical pathways -log(P-value) Ratio Molecules Role of JAK1, JAK2 and TYK2 in interferon 2.51E+00 1.11E201 RAF1,IFNGR2,STAT1 signalling Role of NFAT in regulation of the immune 2.27E+00 3.50E202 GNB1,RAF1,CSNK1G2,CSNK1A1,LYN, response MEF2C,ORAI1 Lysine biosynthesis 2.21E+00 3.12E202 AASDH,AASDHPPT Oestrogen receptor signalling 2.18E+00 4.41E202 PRKDC,RAF1,CCNH,GTF2H1,POLR2I, TRRAP Interferon signalling 2.16E+00 8.33E202 IFIT1,IFNGR2,STAT1 Nucleotide excision repair pathway 2.04E+00 8.57E202 CCNH,GTF2H1,POLR2I

Table S2 Continued.

Ingenuity canonical pathways -log(P-value) Ratio Molecules Calcium signalling 1.66E+00 2.90E202 TPM1,RYR1,TRPC4,MEF2C,TRPC6,MYL3 EGF signalling 1.64E+00 5.77E202 RAF1,STAT1,RASA1 Assembly of RNA polymerase II complex 1.59E+00 5.36E202 CCNH,GTF2H1,POLR2I Phospholipase C signalling 1.57E+00 2.69E202 GNB1,RAF1,LYN,ARHGEF17,MEF2C, MARCKS,MYL3 D-glutamine and D-glutamate metabolism 1.40E+00 3.85E202 GLS Nicotinate and nicotinamide metabolism 1.37E+00 2.96E202 MAP2K6,PRPF4B,CSNK1A1,DYRK1A Lysine degradation 1.34E+00 2.17E202 AASDH,AASDHPPT,MLL3 GM-CSF signalling 1.32E+00 4.48E202 RAF1,LYN,STAT1 Androgen signalling 1.26E+00 2.78E202 GNB1,CCNH,GTF2H1,POLR2I Huntington’s disease signalling 1.24E+00 2.52E202 GNB1,VTI1A,GLS,POLR2I,RASA1,SIN3A Ga12/13 signalling 1.21E+00 3.12E202 RAF1,MEF2C,RASA1,MYL3 PDGF signalling 1.16E+00 3.80E202 RAF1,STAT1,RASA1 Nitrogen metabolism 1.13E+00 1.65E202 GLS,NIT1 Prolactin signalling 1.13E+00 3.75E202 RAF1,CEBPB,STAT1 Oncostatin M signalling 1.11E+00 5.71E202 RAF1,STAT1 Cyclins and cell cycle regulation 1.09E+00 3.37E202 RAF1,CCNH,SIN3A Role of NFAT in cardiac hypertrophy 1.08E+00 2.42E202 MAP2K6,GNB1,RAF1,CSNK1A1,MEF2C Cdc42 signalling 1.07E+00 2.30E202 RAF1,IQGAP1,RASA1,MYL3 Bladder cancer signalling 1.04E+00 3.26E202 RAF1,MMP16,SIN3A Role of PKR in interferon induction and 1.01E+00 4.35E202 MAP2K6,STAT1 antiviral response Cysteine metabolism 9.92E201 2.33E202 CHST2,SRR Nucleotide sugar metabolism 9.85E201 1.54E202 TGDS Inositol phosphate metabolism 9.81E201 2.25E202 MAP2K6,PRPF4B,CSNK1A1,DYRK1A Glucocorticoid receptor signalling 9.41E201 2.03E202 RAF1,CCNH,GTF2H1,CEBPB,STAT1, POLR2I GABA receptor signalling 9.07E201 3.51E202 GABRD,GABRB2 IL-6 signalling 8.89E201 3.00E202 MAP2K6,RAF1,CEBPB CNTF signalling 8.76E201 3.64E202 RAF1,STAT1 CXCR4 signalling 8.64E201 2.37E202 GNB1,RAF1,LYN,MYL3 Cholecystokinin/gastrin-mediated signalling 8.40E201 2.83E202 MAP2K6,RAF1,MEF2C FceRI signalling 8.31E201 2.70E202 MAP2K6,RAF1,LYN Cleavage and polyadenylation of pre-mRNA 8.21E201 8.33E202 NUDT21 Assembly of RNA polymerase III complex 8.21E201 6.67E202 GTF3C2 Cardiac hypertrophy signalling 8.17E201 2.04E202 MAP2K6,GNB1,RAF1,MEF2C,MYL3 Type I diabetes mellitus signalling 8.03E201 2.48E202 MAP2K6,IFNGR2,STAT1 p38 MAPK signalling 8.03E201 2.83E202 MAP2K6,MEF2C,STAT1 Pancreatic adenocarcinoma signalling 7.94E201 2.52E202 RAF1,STAT1,SIN3A Glutamate receptor signalling 7.92E201 2.90E202 GNB1,GLS Thrombopoietin signalling 7.80E201 3.17E202 RAF1,STAT1 Cyanoamino acid metabolism 7.60E201 1.64E202 NIT1 RAN signalling 7.60E201 4.35E202 KPNB1 DNA double-strand break repair by 7.60E201 5.88E202 RAD52 homologous recombination DNA double-strand break repair by 7.60E201 5.26E202 PRKDC non-homologous end joining Mitotic roles of Polo-like kinase 7.55E201 3.12E202 PLK4,ANAPC5 Granzyme B signalling 7.32E201 6.25E202 PRKDC Sulfur metabolism 7.32E201 1.69E202 SUOX Ephrin receptor signalling 7.31E201 2.01E202 GNB1,RAF1,KALRN,RASA1 JAK/Stat signalling 7.09E201 3.12E202 RAF1,STAT1 T helper cell differentiation 6.99E201 2.78E202 IFNGR2,STAT1 Role of MAPK signalling in the 6.99E201 3.08E202 MAP2K6,RAF1 pathogenesis of influenza Role of Wnt/GSK-3b signalling in the 6.88E201 2.47E202 CSNK1G2,CSNK1A1 pathogenesis of influenza Synaptic long-term depression 6.82E201 2.05E202 RAF1,LYN,RYR1 Melatonin signalling 6.78E201 2.60E202 MAP2K6,RAF1 Non-small cell lung cancer signalling 6.78E201 2.53E202 RAF1,SIN3A Neurotrophin/TRK signalling 6.78E201 2.60E202 MAP2K6,RAF1 IL-17 signalling 6.38E201 2.70E202 MAP2K6,CEBPB FLT3 signalling in haematopoietic 6.29E201 2.70E202 RAF1,STAT1 progenitor cells PI3K signalling in B lymphocytes 6.26E201 2.10E202 RAF1,ATF7,LYN DNA methylation and transcriptional 6.22E201 4.35E202 SIN3A repression signalling IL-3 signalling 6.20E201 2.70E202 RAF1,STAT1 LPS-stimulated MAPK signalling 6.02E201 2.44E202 MAP2K6,RAF1 Ceramide signalling 5.76E201 2.30E202 RAF1,SMPD3 Acute myeloid leukaemia signalling 5.76E201 2.44E202 MAP2K6,RAF1 Hepatic fibrosis/hepatic stellate cell activation 5.70E201 2.04E202 IFNGR2,STAT1,MYL3 N-Glycan degradation 5.69E201 3.85E202 MAN2B1 IL-22 signalling 5.69E201 4.00E202 STAT1

Table S2 Continued.

Ingenuity canonical pathways -log(P-value) Ratio Molecules Prostate cancer signalling 5.60E201 2.06E202 RAF1,SIN3A Molecular mechanisms of cancer 5.58E201 1.59E202 MAP2K6,PRKDC,RAF1,ARHGEF17, RASA1,SIN3A B cell receptor signalling 5.47E201 1.92E202 MAP2K6,RAF1,LYN Role of JAK family kinases in IL-6-type 5.39E201 3.70E202 STAT1 cytokine signalling Actin cytoskeleton signalling 5.33E201 1.68E202 RAF1,TMSB10/TMSB4X,IQGAP1,MYL3 IL-15 production 5.24E201 3.12E202 STAT1 Sonic hedgehog signalling 5.24E201 3.03E202 DYRK1A FGF signalling 5.15E201 2.22E202 MAP2K6,RAF1 VEGF signalling 5.15E201 2.02E202 RAF1,ELAVL1 Selenoamino acid metabolism 5.11E201 1.47E202 AHCYL2 Methionine metabolism 5.11E201 1.28E202 AHCYL2 a-Adrenergic signalling 5.08E201 1.90E202 GNB1,RAF1 RANK signalling in osteoclasts 5.08E201 2.11E202 MAP2K6,RAF1 TGF-b signalling 5.08E201 2.25E202 MAP2K6,RAF1 Tight junction signalling 5.04E201 1.83E202 CLDN15,NUDT21,MYL3 Gbc signalling 5.01E201 1.71E202 GNB1,RAF1 Serotonin receptor signalling 4.98E201 2.17E202 HTR5A PAK signalling 4.94E201 1.87E202 RAF1,MYL3 HMGB1 signalling 4.75E201 2.00E202 MAP2K6,IFNGR2 IL-1 signalling 4.75E201 1.87E202 MAP2K6,GNB1 G-protein signalling mediated by tubby 4.73E201 2.44E202 GNB1 Retinol metabolism 4.62E201 1.67E202 BCMO1 Protein kinase A signalling 4.57E201 1.53E202 GNB1,RAF1,ANAPC5,RYR1,MYL3 Chronic myeloid leukaemia signalling 4.56E201 1.90E202 RAF1,SIN3A Role of JAK2 in hormone-like cytokine 4.51E201 2.70E202 STAT1 signalling T cell receptor signalling 4.50E201 1.83E202 RAF1,RASA1 Glioma signalling 4.44E201 1.79E202 RAF1,SIN3A PPARa/RXRa activation 4.41E201 1.63E202 MAP2K6,RAF1,LPL IL-9 signalling 4.40E201 2.50E202 STAT1 IL-12 signalling and production in 4.38E201 1.52E202 CEBPB,STAT1 macrophages IGF-1 signalling 4.32E201 1.87E202 RAF1,RASA1 Neuroprotective role of THOP1 in Alzheimer’s 4.30E201 1.85E202 ECE2 disease IL-17A signalling in fibroblasts 4.30E201 2.50E202 CEBPB Glutamate metabolism 4.30E201 1.33E202 GLS Acute phase response signalling 4.28E201 1.69E202 MAP2K6,RAF1,CEBPB CREB signalling in neurons 4.24E201 1.49E202 GNB1,RAF1,POLR2I Axonal guidance signalling 4.18E201 1.39E202 GNB1,RAF1,KALRN,ROBO3,RASA1, MYL3 fMLP signalling in neutrophils 4.05E201 1.56E202 GNB1,RAF1 Rac signalling 4.05E201 1.63E202 RAF1,IQGAP1 Role of IL-17F in allergic inflammatory 4.01E201 2.17E202 RAF1 airway diseases Corticotropin releasing hormone signalling 3.99E201 1.49E202 RAF1,MEF2C ILK signalling 3.95E201 1.55E202 MAP2K6,TMSB10/TMSB4X,MYL3 NRF2-mediated oxidative stress response 3.91E201 1.55E202 MAP2K6,RAF1,DNAJC1 Renin-angiotensin signalling 3.84E201 1.61E202 RAF1,STAT1 Chondroitin sulfate biosynthesis 3.84E201 1.56E202 CHST2 Galactose metabolism 3.84E201 9.43E203 GANC FcRIIB signalling in B lymphocytes 3.76E201 1.69E202 LYN Melanoma signalling 3.68E201 2.17E202 RAF1 CCR3 signalling in eosinophils 3.60E201 1.57E202 GNB1,RAF1 Type II diabetes mellitus signalling 3.60E201 1.25E202 CEBPB,SMPD3 Keratan sulfate biosynthesis 3.60E201 1.89E202 CHST2 Cell cycle: G2/M DNA damage checkpoint 3.60E201 2.04E202 PRKDC regulation Thrombin signalling 3.55E201 1.46E202 GNB1,RAF1,MYL3 Breast cancer regulation by stathmin1 3.55E201 1.44E202 GNB1,RAF1,ARHGEF17 P2Y purigenic receptor signalling pathway 3.47E201 1.48E202 GNB1,RAF1 Tryptophan metabolism 3.42E201 8.55E203 TDO2,NIT1 Phototransduction pathway 3.38E201 1.54E202 GNB1 p70S6K signalling 3.34E201 1.54E202 RAF1,LYN Nur77 signalling in T lymphocytes 3.31E201 1.59E202 SIN3A GNRH signalling 3.30E201 1.38E202 MAP2K6,RAF1 Amyloid processing 3.24E201 1.79E202 CSNK1A1 CD27 signalling in lymphocytes 3.18E201 1.75E202 MAP2K6 Toll-like receptor signalling 3.18E201 1.82E202 MAP2K6 Activation of IRF by cytosolic pattern 3.05E201 1.39E202 STAT1 recognition receptors cAMP-mediated signalling 3.03E201 1.38E202 RAF1,RGS2,HTR5A

Table S2 Continued.

Ingenuity canonical pathways -log(P-value) Ratio Molecules Endometrial cancer signalling 2.99E201 1.75E202 RAF1 Role of IL-17A in arthritis 2.99E201 1.59E202 MAP2K6 IL-2 signalling 2.93E201 1.72E202 RAF1 Ovarian cancer signalling 2.91E201 1.41E202 RAF1,SIN3A Calcium-induced T lymphocyte apoptosis 2.82E201 1.43E202 ORAI1 Cell cycle: G1/S checkpoint regulation 2.82E201 1.64E202 SIN3A Role of macrophages, fibroblasts and 2.80E201 1.20E202 MAP2K6,RAF1,CSNK1A1,CEBPB endothelial cells in rheumatoid arthritis Role of BRCA1 in DNA samage response 2.77E201 1.64E202 STAT1 Propanoate metabolism 2.77E201 8.26E203 AASDH Starch and sucrose metabolism 2.77E201 5.92E203 GANC Antiproliferative role of somatostatin 2.62E201 1.41E202 GNB1 receptor 2 CCR5 signalling in macrophages 2.52E201 1.06E202 GNB1 IL-15 signalling 2.52E201 1.47E202 RAF1 ERK5 signalling 2.52E201 1.56E202 MEF2C Role of JAK1 and JAK3 in cytokine signalling 2.52E201 1.45E202 STAT1 Tyrosine metabolism 2.52E201 5.08E203 IYD CD40 signalling 2.47E201 1.43E202 MAP2K6 Angiopoietin signalling 2.34E201 1.35E202 RASA1 Glycine, serine and threonine metabolism 2.34E201 6.90E203 SRR Erythropoietin signalling 2.30E201 1.28E202 RAF1 Germ cell-sertoli cell junction signalling 2.28E201 1.20E202 MAP2K6,IQGAP1 IL-10 signalling 2.26E201 1.28E202 MAP2K6 Growth hormone signalling 2.26E201 1.33E202 STAT1 Renal cell carcinoma signalling 2.26E201 1.35E202 RAF1 Aldosterone signalling in epithelial sells 2.25E201 1.18E202 RAF1,DNAJC1 Sphingolipid metabolism 2.22E201 9.17E203 SMPD3 Arginine and proline metabolism 2.22E201 5.65E203 P4HA1 Chemokine signalling 2.18E201 1.35E202 RAF1 Small cell lung cancer signalling 2.14E201 1.12E202 SIN3A BMP signalling pathway 2.10E201 1.25E202 RAF1 NF-kB activation by viruses 2.03E201 1.22E202 RAF1 LXR/RXR activation 1.99E201 1.08E202 LPL