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Gene Symbol Probe Set Fold Change Parametric Description Map Genbank Unigene AI/AD P-Value Accession Cluster

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Supplemental Table. Unabridged List of Genes Differentially Expressed Between AD and AI Prostate Cancer (Best, C.J.M., et al.) Gene Symbol Probe Set Fold Change Parametric Description Map GenBank UniGene AI/AD p-value Accession Cluster AP2A2 215764_x_at 0.60 0.0001 adaptor-related protein complex 2, alpha 2 subunit 11p15.5 AA877641 Hs.19121 ADORA2A 205013_s_at 0.69 0.0030 adenosine A2a receptor 22q11.23 NM_000675.2 Hs.197029 ADPRTL2 215773_x_at 1.41 0.0039 ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2 14q11.2-q12 AJ236912.1 Hs.409412 AKR7A2 202139_at 0.62 0.0006 aldo-keto reductase family 7, member A2 (aflatoxin aldehyde 1p35.1-p36.23 NM_003689.1 Hs.6980 reductase) STAT5B 212550_at 0.71 0.0001 signal transducer and activator of transcription 5B 17q11.2 AL080218.1 Hs.434992 ST3GALVI 213355_at 3.44 0.0045 alpha2,3-sialyltransferase 3q12.2 AK001922.1 Hs.440913 A2M 217757_at 2.07 0.0030 alpha-2-macroglobulin 12p13.3-p12.3 NM_000014.3 Hs.74561 ALS2CR3 202125_s_at 1.72 0.0006 amyotrophic lateral sclerosis 2 (juvenile) chromosome region, 2q33 NM_015049.1 Hs.154248 candidate 3 ASPN 219087_at 2.87 0.0017 asporin (LRR class 1) 9q22 NM_017680.1 Hs.435655 ATP5L 208746_x_at 0.68 0.0030 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit g 11q23 AF070655.1 Hs.107476 ATP6V0B 200078_s_at 0.60 0.0018 ATPase, H+ transporting, lysosomal 21kDa, V0 subunit c'' 1p32.3 BC005876.1 Hs.7476 ABCG2 209735_at 1.87 0.0014 ATP-binding cassette, sub-family G (WHITE), member 2 4q22 AF098951.2 Hs.194720 BAIAP2 209502_s_at 0.40 0.0012 BAI1-associated protein 2 17q25 BC002495.1 Hs.188332 BLZF1 32088_at 2.67 0.0025 basic leucine zipper nuclear factor 1 (JEM-1) 1q24 U79751 Hs.444697 BCKDK 202030_at 0.57 0.0004 branched chain alpha-ketoacid dehydrogenase kinase 16p11.2 NM_005881.1 Hs.20644 BIN3 222199_s_at 0.62 0.0027 bridging integrator 3 8p21.2 AK001289.1 Hs.68090 BTG2 201236_s_at 0.50 0.0021 BTG family, member 2 1q32 NM_006763.1 Hs.75462 BPAG1 212254_s_at 2.78 0.0001 bullous pemphigoid antigen 1, 230/240kDa 6p12-p11 BG253119 Hs.443518 BPAG1 215016_x_at 2.54 0.0002 bullous pemphigoid antigen 1, 230/240kDa 6p12-p11 BC004912.1 Hs.443518 SHAPY 46323_at 0.57 0.0046 Ca2+-dependent endoplasmic reticulum nucleoside diphosphatase 17q25.3 AL120741 Hs.8859 CDH11 207173_x_at 3.10 0.0004 cadherin 11, type 2, OB-cadherin (osteoblast) 16q22.1 D21254.1 Hs.443435 CPT2 204264_at 0.60 0.0026 carnitine palmitoyltransferase II 1p32 NM_000098.1 Hs.274336 CD84 211189_x_at 0.58 0.0032 CD84 antigen (leukocyte antigen) 1q24 AF054816.1 Hs.398093 GRIM19 220864_s_at 0.21 0.0020 cell death-regulatory protein GRIM19 19p13.2 NM_015965.1 Hs.279574 CGI-12 219363_s_at 2.54 0.0030 CGI-12 protein 8q22.1 NM_015942.1 Hs.46680 CGI-130 203259_s_at 1.61 0.0038 CGI-130 protein 6q13-q24.3 BC001671.1 Hs.32826 PNAS-4 212371_at 1.92 0.0003 CGI-146 protein 1q44 AL049397.1 Hs.211473 CCR9 207445_s_at 0.65 0.0031 chemokine (C-C motif) receptor 9 3p21.3 AF145439.1 Hs.225946 CXCR6 206974_at 0.67 0.0039 chemokine (C-X-C motif) receptor 6 3p21 NM_006564.1 Hs.34526 CSPG2 204619_s_at 3.10 0.0010 chondroitin sulfate proteoglycan 2 (versican) 5q14.3 BF590263 Hs.434488 C11orf10 218213_s_at 0.46 0.0023 chromosome 11 open reading frame 10 11q12-q13.1 NM_014206.1 Hs.437779 C11orf2 217969_at 0.63 0.0018 chromosome 11 open reading frame2 11q13 NM_013265.2 Hs.277517 C14orf2 210532_s_at 0.68 0.0033 chromosome 14 open reading frame 2 14q32.33 AF116639.1 Hs.109052 C14orf58 219316_s_at 0.67 0.0032 chromosome 14 open reading frame 58 14q24.3 NM_017791.1 Hs.267566 C2orf3 216305_s_at 1.72 0.0021 chromosome 2 open reading frame 3 2p11.2-p11.1 AC005034 Hs.158969 C21orf97 218018_at 0.58 0.0048 chromosome 21 open reading frame 97 21q22.3 NM_021941.1 Hs.458335 C22orf4 33778_at 0.67 0.0008 chromosome 22 open reading frame 4 22q13.3 AL096779 Hs.20017 C5orf6 218023_s_at 0.62 0.0008 chromosome 5 open reading frame 6 5q31 NM_016605.1 Hs.54056 LUC7A 220044_x_at 2.75 0.0007 cisplatin resistance-associated overexpressed protein 17q21 NM_016424.1 Hs.130293 COL5A2 221729_at 2.30 0.0043 collagen, type V, alpha 2 2q14-q32 NM_000393.1 Hs.283393 COL15A1 203477_at 2.67 0.0006 collagen, type XV, alpha 1 9q21-q22 NM_001855.1 Hs.409034 COPS6 213504_at 0.72 0.0032 COP9 subunit 6 (MOV34 homolog, 34 kD) 7q22.1 W63732 Hs.15591 CXADR 203917_at 0.57 0.0048 coxsackie virus and adenovirus receptor 21q21.1 NM_001338.1 Hs.79187 DMTF1 203301_s_at 1.90 0.0012 cyclin D binding myb-like transcription factor 1 7q21 NM_021145.1 Hs.129506 COX7C 217491_x_at 0.51 0.0041 cytochrome c oxidase subunit VIIc 5q14 AF042165 Hs.430075 COX8 201119_s_at 0.57 0.0024 cytochrome c oxidase subunit VIII 11q12-q13 NM_004074.1 Hs.433901 DBP 209783_at 0.63 0.0003 D site of albumin promoter (albumin D-box) binding protein 19q13.3 D28468.1 Hs.414480 DC13 218447_at 0.52 0.0035 DC13 protein 16q23.2 NM_020188.1 Hs.6879 DSS1 202276_at 0.63 0.0040 Deleted in split-hand/split-foot 1 region 7q21.3-q22.1 NM_006304.1 Hs.333495 DBI 209389_x_at 0.58 0.0001 diazepam binding inhibitor (GABA receptor modulator, acyl- 2q12-q21 M15887.1 Hs.78888 Coenzyme A binding protein) DKFZp547P234 221865_at 0.64 0.0040 DKFZp547P234 protein 9q33.1 BF969986 Hs.170226 DKFZP564O0823 204687_at 0.58 0.0008 DKFZP564O0823 protein 4q13.3-q21.3 NM_015393.1 Hs.105460 DKFZP566H073 212047_s_at 0.72 0.0049 DKFZP566H073 protein 17p13.3 AK025329.1 Hs.7158 EDG4 206723_s_at 0.57 0.0043 endothelial differentiation, lysophosphatidic acid G-protein-coupled 19p12 AF011466.1 Hs.122575 receptor, 4 EIF3S9 203462_x_at 0.65 0.0001 eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa 7p22.3 NM_003751.1 Hs.371001 EIF4EL3 213571_s_at 0.73 0.0027 eukaryotic translation initiation factor 4E-like 3 2q37.1 BF516289 Hs.211823 XPO1 208775_at 1.62 0.0046 exportin 1 (CRM1 homolog, yeast) 2p16 D89729.1 Hs.157367 ECM2 206101_at 2.25 0.0040 extracellular matrix protein 2, female organ and adipocyte specific 9q22.3 NM_001393.1 Hs.117060 FBXO11 203255_at 1.95 0.0009 F-box only protein 11 2p21 NM_018693.1 Hs.284289 FBXO3 218432_at 2.10 0.0049 F-box only protein 3 11p13 NM_012175.1 Hs.406787 FN1 212464_s_at 2.53 0.0005 fibronectin 1 2q34 X02761.1 Hs.418138 FN1 211719_x_at 2.72 0.0007 fibronectin 1 2q34 BC005858.1 Hs.418138 FN1 210495_x_at 1.86 0.0013 fibronectin 1 2q34 AF130095.1 Hs.418138 FRAT2 209864_at 0.65 0.0017 frequently rearranged in advanced T-cell lymphomas 2 10q24.1 AB045118.1 Hs.140720 X123 213900_at 0.34 0.0011 Friedreich ataxia region gene X123 9q13-q21 AA524029 Hs.77889 GPR116 212950_at 2.40 0.0044 G protein-coupled receptor 116 6p21.1 AB018301.1 Hs.362806 GABARAPL3 211458_s_at 0.52 0.0014 GABA(A) receptors associated protein like 3 15q26.1 AF180519.1 Hs.334497 GMPPB 219920_s_at 0.63 0.0019 GDP-mannose pyrophosphorylase B 3p21.31 NM_021971.1 Hs.438691 GTF3C3 218343_s_at 1.60 0.0033 general transcription factor IIIC, polypeptide 3, 102kDa 2q33.1 NM_012086.1 Hs.253724 GL004 219137_s_at 1.69 0.0015 GL004 protein 2q36.3 NM_020194.1 Hs.105166 G6PT1 202830_s_at 0.58 0.0024 glucose-6-phosphatase, transport (glucose-6-phosphate) protein 1 11q23.3 NM_001467.1 Hs.132760 GFPT1 202721_s_at 0.60 0.0006 glutamine-fructose-6-phosphate transaminase 1 2p13 BE645771 Hs.1674 GREB1 205862_at 0.18 0.0019 GREB1 protein 2p25.1 NM_014668.1 Hs.438037 GADD45B 209304_x_at 0.26 0.0030 growth arrest and DNA-damage-inducible, beta 19p13.3 AF087853.1 Hs.110571 GADD45B 207574_s_at 0.28 0.0031 growth arrest and DNA-damage-inducible, beta 19p13.3 NM_015675.1 Hs.110571 GADD45G 204121_at 0.23 0.0001 growth arrest and DNA-damage-inducible, gamma 9q22.1-q22.2 NM_006705.2 Hs.9701 GMPR 204187_at 0.57 0.0036 guanosine monophosphate reductase 6p23 NM_006877.1 Hs.1435 HNRPA0 201055_s_at 0.65 0.0007 heterogeneous nuclear ribonucleoprotein A0 5q31 NM_006805.1 Hs.96996 HNRPH3 208990_s_at 1.73 0.0011 heterogeneous nuclear ribonucleoprotein H3 (2H9) 10q22 AF132362.1 Hs.156481 D13S106E 204190_at 1.80 0.0002 highly charged protein 13q12-q14 NM_005800.1 Hs.291431 HINT1 208826_x_at 0.66 0.0007 histidine triad nucleotide binding protein 1 5q31.2 U27143.1 Hs.256697 HOP 211597_s_at 1.89 0.0028 homeodomain-only protein 4q11-q12 AB059408.1 Hs.13775 222148_s_at 1.27 0.0015 Homo sapiens mRNA; cDNA DKFZp434I212 (from clone 17 BF688108 Hs.436453 DKFZp434I212) 221844_x_at 0.50 0.0000 Homo sapiens transcribed sequence with moderate similarity to 4 AV756161 Hs.508129 protein ref:NP_060312.1 (H.sapiens) hypothetical protein FLJ20489 [Homo sapiens] 213931_at 0.29 0.0017 Homo sapiens transcribed sequence with strong similarity to protein AI819238 Hs.502810 pir:A40227 (H.sapiens) A40227 transcription repressor Id-2 - human 215088_s_at 0.78 0.0034 Homo sapiens transcribed sequence with strong similarity to protein BG110532 Hs.355964 ref:NP_002992.1 (H.sapiens) succinate dehydrogenase complex, subunit C precursor; Succinate dehydrogenase complex, subunit C, integral membrane protein,; succinate-ubiquinone oxidoreduca 214351_x_at 0.45 0.0020 Homo sapiens transcribed sequence with strong similarity to protein 16 AA789278 Hs.410817 ref:NP_150254.1 (H.sapiens) ribosomal protein L13; 60S ribosomal protein L13; breast basic conserved protein 1 [Homo sapiens] 55705_at 0.70 0.0048 Homo sapiens transcribed sequences W07773 Hs.498224 221803_s_at 2.44 0.0023 Homo sapiens, nuclear receptor binding factor-2, clone 10 AA883074 Hs.27181 IMAGE:3463191, mRNA HERPUD1 217168_s_at 0.72 0.0012 homocysteine-inducible, endoplasmic reticulum stress-inducible, 16q12.2-q13 AF217990.1 Hs.146393 ubiquitin-like domain member 1 HGD 214307_at 0.33 0.0001 homogentisate 1,2-dioxygenase (homogentisate
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    bioRxiv preprint doi: https://doi.org/10.1101/551978; this version posted February 26, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 A high-resolution, chromosome-assigned Komodo dragon genome reveals adaptations in the 2 cardiovascular, muscular, and chemosensory systems of monitor lizards 3 4 Abigail L. Lind1, Yvonne Y.Y. Lai2, Yulia Mostovoy2, Alisha K. Holloway1, Alessio Iannucci3, Angel 5 C.Y. Mak2, Marco Fondi3, Valerio Orlandini3, Walter L. Eckalbar4, Massimo Milan5, Michail 6 Rovatsos6,7, , Ilya G. Kichigin8, Alex I. Makunin8, Martina J. Pokorná6, Marie Altmanová6, Vladimir 7 A. Trifonov8, Elio Schijlen9, Lukáš Kratochvíl6, Renato Fani3, Tim S. Jessop10, Tomaso Patarnello5, 8 James W. Hicks11, Oliver A. Ryder12, Joseph R. Mendelson III13,14, Claudio Ciofi3, Pui-Yan 9 Kwok2,4,15, Katherine S. Pollard1,4,16,17,18, & Benoit G. Bruneau1,2,19 10 11 1. Gladstone Institutes, San Francisco, CA 94158, USA. 12 2. Cardiovascular Research Institute, University of California, San Francisco, CA 94143, USA. 13 3. Department of Biology, University of Florence, 50019 Sesto Fiorentino (FI), Italy 14 4. Institute for Human Genetics, University of California, San Francisco, CA 94143, USA. 15 5. Department of Comparative Biomedicine and Food Science, University of Padova, 35020 16 Legnaro (PD), Italy 17 6. Department of Ecology, Charles University, 128 00 Prague, Czech Republic 18 7. Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, 277 21 19 Liběchov, Czech Republic 20 8.
  • Snapshot: the Splicing Regulatory Machinery Mathieu Gabut, Sidharth Chaudhry, and Benjamin J

    Snapshot: the Splicing Regulatory Machinery Mathieu Gabut, Sidharth Chaudhry, and Benjamin J

    192 Cell SnapShot: The Splicing Regulatory Machinery Mathieu Gabut, Sidharth Chaudhry, and Benjamin J. Blencowe 133 Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada Expression in mouse , April4, 2008©2008Elsevier Inc. Low High Name Other Names Protein Domains Binding Sites Target Genes/Mouse Phenotypes/Disease Associations Amy Ceb Hip Hyp OB Eye SC BM Bo Ht SM Epd Kd Liv Lu Pan Pla Pro Sto Spl Thy Thd Te Ut Ov E6.5 E8.5 E10.5 SRp20 Sfrs3, X16 RRM, RS GCUCCUCUUC SRp20, CT/CGRP; −/− early embryonic lethal E3.5 9G8 Sfrs7 RRM, RS, C2HC Znf (GAC)n Tau, GnRH, 9G8 ASF/SF2 Sfrs1 RRM, RS RGAAGAAC HipK3, CaMKIIδ, HIV RNAs; −/− embryonic lethal, cond. KO cardiomyopathy SC35 Sfrs2 RRM, RS UGCUGUU AChE; −/− embryonic lethal, cond. KO deficient T-cell maturation, cardiomyopathy; LS SRp30c Sfrs9 RRM, RS CUGGAUU Glucocorticoid receptor SRp38 Fusip1, Nssr RRM, RS ACAAAGACAA CREB, type II and type XI collagens SRp40 Sfrs5, HRS RRM, RS AGGAGAAGGGA HipK3, PKCβ-II, Fibronectin SRp55 Sfrs6 RRM, RS GGCAGCACCUG cTnT, CD44 DOI 10.1016/j.cell.2008.03.010 SRp75 Sfrs4 RRM, RS GAAGGA FN1, E1A, CD45; overexpression enhances chondrogenic differentiation Tra2α Tra2a RRM, RS GAAARGARR GnRH; overexpression promotes RA-induced neural differentiation SR and SR-Related Proteins Tra2β Sfrs10 RRM, RS (GAA)n HipK3, SMN, Tau SRm160 Srrm1 RS, PWI AUGAAGAGGA CD44 SWAP Sfrs8 RS, SWAP ND SWAP, CD45, Tau; possible asthma susceptibility gene hnRNP A1 Hnrnpa1 RRM, RGG UAGGGA/U HipK3, SMN2, c-H-ras; rheumatoid arthritis, systemic lupus
  • CDH12 Cadherin 12, Type 2 N-Cadherin 2 RPL5 Ribosomal

    CDH12 Cadherin 12, Type 2 N-Cadherin 2 RPL5 Ribosomal

    5 6 6 5 . 4 2 1 1 1 2 4 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 A A A A A A A A A A A A A A A A A A A A C C C C C C C C C C C C C C C C C C C C R R R R R R R R R R R R R R R R R R R R B , B B B B B B B B B B B B B B B B B B B , 9 , , , , 4 , , 3 0 , , , , , , , , 6 2 , , 5 , 0 8 6 4 , 7 5 7 0 2 8 9 1 3 3 3 1 1 7 5 0 4 1 4 0 7 1 0 2 0 6 7 8 0 2 5 7 8 0 3 8 5 4 9 0 1 0 8 8 3 5 6 7 4 7 9 5 2 1 1 8 2 2 1 7 9 6 2 1 7 1 1 0 4 5 3 5 8 9 1 0 0 4 2 5 0 8 1 4 1 6 9 0 0 6 3 6 9 1 0 9 0 3 8 1 3 5 6 3 6 0 4 2 6 1 0 1 2 1 9 9 7 9 5 7 1 5 8 9 8 8 2 1 9 9 1 1 1 9 6 9 8 9 7 8 4 5 8 8 6 4 8 1 1 2 8 6 2 7 9 8 3 5 4 3 2 1 7 9 5 3 1 3 2 1 2 9 5 1 1 1 1 1 1 5 9 5 3 2 6 3 4 1 3 1 1 4 1 4 1 7 1 3 4 3 2 7 6 4 2 7 2 1 2 1 5 1 6 3 5 6 1 3 6 4 7 1 6 5 1 1 4 1 6 1 7 6 4 7 e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m
  • Genetic and Pharmacological Approaches to Preventing Neurodegeneration

    Genetic and Pharmacological Approaches to Preventing Neurodegeneration

    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2012 Genetic and Pharmacological Approaches to Preventing Neurodegeneration Marco Boccitto University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Neuroscience and Neurobiology Commons Recommended Citation Boccitto, Marco, "Genetic and Pharmacological Approaches to Preventing Neurodegeneration" (2012). Publicly Accessible Penn Dissertations. 494. https://repository.upenn.edu/edissertations/494 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/494 For more information, please contact [email protected]. Genetic and Pharmacological Approaches to Preventing Neurodegeneration Abstract The Insulin/Insulin-like Growth Factor 1 Signaling (IIS) pathway was first identified as a major modifier of aging in C.elegans. It has since become clear that the ability of this pathway to modify aging is phylogenetically conserved. Aging is a major risk factor for a variety of neurodegenerative diseases including the motor neuron disease, Amyotrophic Lateral Sclerosis (ALS). This raises the possibility that the IIS pathway might have therapeutic potential to modify the disease progression of ALS. In a C. elegans model of ALS we found that decreased IIS had a beneficial effect on ALS pathology in this model. This beneficial effect was dependent on activation of the transcription factor daf-16. To further validate IIS as a potential therapeutic target for treatment of ALS, manipulations of IIS in mammalian cells were investigated for neuroprotective activity. Genetic manipulations that increase the activity of the mammalian ortholog of daf-16, FOXO3, were found to be neuroprotective in a series of in vitro models of ALS toxicity.