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Supplementary Table 1: Genes Located on Chromosome 18P11-18Q23, an Area Significantly Linked to TMPRSS2-ERG Fusion

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Supplementary Table 1: Genes located on Chromosome 18p11-18q23, an area significantly linked to TMPRSS2-ERG fusion Symbol Cytoband Description LOC260334 18p11 HSA18p11 beta-tubulin 4Q pseudogene IL9RP4 18p11.3 interleukin 9 receptor pseudogene 4 LOC100132166 18p11.32 hypothetical LOC100132166 similar to Rho-associated protein kinase 1 (Rho- associated, coiled-coil-containing protein kinase 1) (p160 LOC727758 18p11.32 ROCK-1) (p160ROCK) (NY-REN-35 antigen) ubiquitin specific peptidase 14 (tRNA-guanine USP14 18p11.32 transglycosylase) THOC1 18p11.32 THO complex 1 COLEC12 18pter-p11.3 collectin sub-family member 12 CETN1 18p11.32 centrin, EF-hand protein, 1 CLUL1 18p11.32 clusterin-like 1 (retinal) C18orf56 18p11.32 chromosome 18 open reading frame 56 TYMS 18p11.32 thymidylate synthetase ENOSF1 18p11.32 enolase superfamily member 1 YES1 18p11.31-p11.21 v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1 LOC645053 18p11.32 similar to BolA-like protein 2 isoform a similar to 26S proteasome non-ATPase regulatory LOC441806 18p11.32 subunit 8 (26S proteasome regulatory subunit S14) (p31) ADCYAP1 18p11 adenylate cyclase activating polypeptide 1 (pituitary) LOC100130247 18p11.32 similar to cytochrome c oxidase subunit VIc LOC100129774 18p11.32 hypothetical LOC100129774 LOC100128360 18p11.32 hypothetical LOC100128360 METTL4 18p11.32 methyltransferase like 4 LOC100128926 18p11.32 hypothetical LOC100128926 NDC80 homolog, kinetochore complex component (S. NDC80 18p11.32 cerevisiae) LOC100130608 18p11.32 hypothetical LOC100130608 structural maintenance of chromosomes flexible hinge SMCHD1 18p11.32 domain containing 1 EMILIN2 18p11.3 elastin microfibril interfacer 2 LPIN2 18p11.31 lipin 2 similar to cysteine and histidine-rich domain (CHORD)- LOC727896 18p11.31 containing, zinc binding protein 1 MYOM1 18p11.31 myomesin 1, 185kDa LOC727918 18p11.31 hypothetical protein LOC727918 MRCL3 18p11.31 myosin regulatory light chain MRCL3 MRLC2 18p11.31 myosin regulatory light chain MRLC2 IGLJCOR18 18p11.31 immunoglobulin lambda joining-constant/OR18 TGIF1 18p11.3 TGFB-induced factor homeobox 1 LOC100129468 18p11.31 hypothetical LOC100129468 LOC100129041 18p11.31 hypothetical protein LOC100129041 DLGAP1 18p11.3 discs, large (Drosophila) homolog-associated protein 1 FLJ35776 18p11.31 hypothetical protein LOC649446 GAPDHL11 18p11.31 glyceraldehyde-3-phosphate dehydrogenase-like 11 LOC284215 18p11.31 hypothetical protein LOC284215 PPIAP14 18p11.31 peptidylprolyl isomerase A (cyclophilin A) pseudogene 14 LOC100129355 18p11.31 hypothetical LOC100129355 LOC642597 18p11.31 hypothetical LOC642597 C18orf18 18p11.31 chromosome 18 open reading frame 18 LOC339290 18p11.31 hypothetical protein LOC339290 ZFP161 18pter-p11.2 zinc finger protein 161 homolog (mouse) LOC100132679 18p11.31 hypothetical protein LOC100132679 EPB41L3 18p11.32 erythrocyte membrane protein band 4.1-like 3 LOC645355 18p11.31 hypothetical LOC645355 TTMA 18p11.31 two transmembrane domain family member A LOC729309 18p11.31 hypothetical protein LOC729309 L3MBTL4 18p11.31 l(3)mbt-like 4 (Drosophila) similar to 60S ribosomal protein L6 (TAX-responsive enhancer element-binding protein 107) (TAXREB107) LOC645387 18p11.31 (Neoplasm-related protein C140) LOC100130480 18p11.31 hypothetical protein LOC100130480 ARHGAP28 18p11.31 Rho GTPase activating protein 28 FLJ38028 18p11.31 hypothetical gene supported by AK095347 LAMA1 18p11.31 laminin, alpha 1 LOC645423 18p11.31 similar to mitochondrial carrier triple repeat 1 LRRC30 18p11.23 leucine rich repeat containing 30 PTPRM 18p11.2 protein tyrosine phosphatase, receptor type, M LOC100128219 18p11.23 hypothetical protein LOC100128219 FLJ11996 18p11.23 hypothetical protein FLJ11996 LOC729391 18p11.23 similar to ring finger and WD repeat domain 2 isoform a LOC100129769 18p11.22 hypothetical LOC100129769 RAB12 18p11.22 RAB12, member RAS oncogene family KIAA0802 18p11.22 KIAA0802 LOC645573 18p11.22 similar to 40S ribosomal protein S4, X isoform NADH dehydrogenase (ubiquinone) flavoprotein 2, NDUFV2 18p11.31-p11.2 24kDa ANKRD12 18p11.22 ankyrin repeat domain 12 TWSG1 18p11.3 twisted gastrulation homolog 1 (Drosophila) RALBP1 18p11.3 ralA binding protein 1 LOC100129773 18p11.22 hypothetical protein LOC100129773 PPP4R1 18p11.22 protein phosphatase 4, regulatory subunit 1 KRT18P8 18p11.22 keratin 18 pseudogene 8 LOC100128925 18p11.22 hypothetical LOC100128925 RAB31 18p11.3 RAB31, member RAS oncogene family TXNDC2 18p11.31-p11.2 thioredoxin domain-containing 2 (spermatozoa) VAMP (vesicle-associated membrane protein)- VAPA 18p11.22 associated protein A, 33kDa APCDD1 18p11.22 adenomatosis polyposis coli down-regulated 1 LOC100130468 18p11.22 hypothetical protein LOC100130468 N-ethylmaleimide-sensitive factor attachment protein, NAPG 18p11.22 gamma LOC645859 18p11.22 similar to coiled-coil domain containing 58 LOC390831 18p11.22 similar to Phosphomannomutase 2 (PMM 2) FAM38B 18p11.22 family with sequence similarity 38, member B LOC100128238 18p11.22 hypothetical LOC100128238 LOC100130329 18p11.21 hypothetical LOC100130329 LOC729589 18p11.21 hypothetical protein LOC729589 AMAC1L1 18p11.21 acyl-malonyl condensing enzyme 1-like 1 LOC729602 18p11.21 similar to nuclear pore complex interacting protein guanine nucleotide binding protein (G protein), alpha GNAL 18p11.22-p11.21 activating activity polypeptide, olfactory type CHMP1B 18p11.21 chromatin modifying protein 1B MPPE1 18p11.21 metallophosphoesterase 1 IMPA2 18p11.2 inositol(myo)-1(or 4)-monophosphatase 2 similar to single stranded DNA binding protein 4 isoform LOC646044 18p11.21 a similar to Probable G-protein coupled receptor 125 LOC728211 18p11.21 precursor similar to nuclear factor of kappa light polypeptide gene LOC646053 18p11.21 enhancer in B-cells 2 (p49/p100) DKFZp779B1634 18p11.21 similar to KIAA1074 protein LOC646065 18p11.21 similar to Phosphomannomutase 2 (PMM 2) LOC732448 18p11.21 similar to coiled-coil domain containing 58 CIDEA 18p11.21 cell death-inducing DFFA-like effector a TUBB6 18p11.21 tubulin, beta 6 AFG3L2 18p11 AFG3 ATPase family gene 3-like 2 (yeast) SLMO1 18p11.21 slowmo homolog 1 (Drosophila) SPIRE1 18p11.21 spire homolog 1 (Drosophila) LOC100131036 18p11.21 hypothetical LOC100131036 CEP76 18p11.21 centrosomal protein 76kDa proteasome (prosome, macropain) assembly chaperone PSMG2 18p11.21 2 PTPN2 18p11.3-p11.2 protein tyrosine phosphatase, non-receptor type 2 LOC100130404 18p11.21 hypothetical LOC100130404 LOC646171 18p11.21 similar to eukaryotic translation initiation factor 4A2 SEH1L 18p11.21 SEH1-like (S. cerevisiae) CEP192 18p11.21 centrosomal protein 192kDa LOC646203 18p11.21 similar to muscle protein684 LOC100130487 18p11.21 hypothetical LOC100130487 C18orf1 18p11.2 chromosome 18 open reading frame 1 C18orf15 18p11.21 chromosome 18 open reading frame 15 C18orf19 18p11.21 chromosome 18 open reading frame 19 RNMT 18p11.22-p11.23 RNA (guanine-7-) methyltransferase MC5R 18p11.2 melanocortin 5 receptor MC2R 18p11.2 melanocortin 2 receptor (adrenocorticotropic hormone) LOC284230 18p11.21 similar to large subunit ribosomal protein L36a LOC100128776 18p11.21 hypothetical LOC100128776 ZNF519 18p11.21 zinc finger protein 519 LOC100131282 18p11.21 hypothetical LOC100131282 MGC26718 18p11.21 similar to ankyrin repeat domain 20A LOC729774 18p11.21 similar to Protein C21orf70 homolog LOC646359 18p11.21 similar to telomeric repeat binding factor 1 isoform 2 LOC390834 18p11.21 similar to fem-1 homolog a LOC100132255 18p11.21 similar to hCG1734082 LOC729804 18p11.21 hypothetical protein LOC729804 similar to coxsackie virus and adenovirus receptor LOC440224 18p11.21 precursor A26B2 18p11.21 ANKRD26-like family B, member 2 olfactory receptor, family 4, subfamily K, member 7 OR4K7P 18p11.21 pseudogene olfactory receptor, family 4, subfamily K, member 8 OR4K8P 18p11.21 pseudogene LOC646442 18p11.21 sorting nexin 19 pseudogene ANKRD30B 18p11.21 ankyrin repeat domain 30B FGF7P1 18p11.21 fibroblast growth factor 7 pseudogene 1 LOC647983 18p11.21 hypothetical protein LOC647983 LOC441811 18p11.21 similar to TBC1 domain family, member 3 LOC284269 18p11.21 similar to C9orf86 LOC100131500 18p11.21 similar to C21orf94 protein LOC100130055 18p11.21 similar to kinase suppressor of ras 1 LOC729863 18p11.21 similar to zinc finger protein 43 (HTF6) LOC644669 18p11.21 hypothetical LOC644669 ROCK1 18q11.1 Rho-associated, coiled-coil containing protein kinase 1 LOC100129157 18q11.1 similar to PRO0435 LOC440487 18q11.1 similar to ribosomal protein L21 LOC100128324 18q11.1 hypothetical LOC100128324 KIAA1772 18q11.1-q11.2 KIAA1772 ESCO1 18q11.2 establishment of cohesion 1 homolog 1 (S. cerevisiae) SNRPD1 18q11.2 small nuclear ribonucleoprotein D1 polypeptide 16kDa ABHD3 18q11.2 abhydrolase domain containing 3 MIB1 18q11.2 mindbomb homolog 1 (Drosophila) MIRN133A1 18q11.2 microRNA 133a-1 MIRN1-2 18q11.2 microRNA 1-2 LOC100128893 18q11.2 hypothetical protein LOC100128893 LOC728473 18q11.2 hypothetical protein LOC728473 GATA6 18q11.1-q11.2 GATA binding protein 6 LOC100131966 18q11.2 hypothetical protein LOC100131966 CTAGE1 18p11.2 cutaneous T-cell lymphoma-associated antigen 1 LOC100128018 18q11.2 similar to CTAGE-1 protein LOC646583 18q11.2 similar to 40S ribosomal protein S4, X isoform similar to Ubiquitin-conjugating enzyme E2 C (Ubiquitin- LOC646595 18q11.2 protein ligase C) (Ubiquitin carrier protein C) (UbcH10) RBBP8 18q11.2 retinoblastoma binding protein 8 CABLES1 18q11.2 Cdk5 and Abl enzyme substrate 1 C18orf45 18q11.2 chromosome 18 open reading frame 45 RIOK3 18q11.2 RIO kinase 3 (yeast) C18orf8 18q11.2 chromosome
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    Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2

    Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491
  • Evidence for Differential Alternative Splicing in Blood of Young Boys With

    Evidence for Differential Alternative Splicing in Blood of Young Boys With

    Stamova et al. Molecular Autism 2013, 4:30 http://www.molecularautism.com/content/4/1/30 RESEARCH Open Access Evidence for differential alternative splicing in blood of young boys with autism spectrum disorders Boryana S Stamova1,2,5*, Yingfang Tian1,2,4, Christine W Nordahl1,3, Mark D Shen1,3, Sally Rogers1,3, David G Amaral1,3 and Frank R Sharp1,2 Abstract Background: Since RNA expression differences have been reported in autism spectrum disorder (ASD) for blood and brain, and differential alternative splicing (DAS) has been reported in ASD brains, we determined if there was DAS in blood mRNA of ASD subjects compared to typically developing (TD) controls, as well as in ASD subgroups related to cerebral volume. Methods: RNA from blood was processed on whole genome exon arrays for 2-4–year-old ASD and TD boys. An ANCOVA with age and batch as covariates was used to predict DAS for ALL ASD (n=30), ASD with normal total cerebral volumes (NTCV), and ASD with large total cerebral volumes (LTCV) compared to TD controls (n=20). Results: A total of 53 genes were predicted to have DAS for ALL ASD versus TD, 169 genes for ASD_NTCV versus TD, 1 gene for ASD_LTCV versus TD, and 27 genes for ASD_LTCV versus ASD_NTCV. These differences were significant at P <0.05 after false discovery rate corrections for multiple comparisons (FDR <5% false positives). A number of the genes predicted to have DAS in ASD are known to regulate DAS (SFPQ, SRPK1, SRSF11, SRSF2IP, FUS, LSM14A). In addition, a number of genes with predicted DAS are involved in pathways implicated in previous ASD studies, such as ROS monocyte/macrophage, Natural Killer Cell, mTOR, and NGF signaling.