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Supplementary Table 1. List of Genes Up-Regulated in Abiraterone-Resistant Vcap Xenograft Samples PIK3IP1 Phosphoinositide-3-Kin

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Supplementary Table 1. List of genes up-regulated in abiraterone-resistant VCaP xenograft samples PIK3IP1 phosphoinositide-3-kinase interacting protein 1 TMEM45A transmembrane protein 45A THBS1 thrombospondin 1 C7orf63 chromosome 7 open reading frame 63 OPTN optineurin FAM49A family with sequence similarity 49, member A APOL4 apolipoprotein L, 4 C17orf108|LOC201229 chromosome 17 open reading frame 108 | hypothetical protein LOC201229 SNORD94 small nucleolar RNA, C/D box 94 PCDHB11 protocadherin beta 11 RBM11 RNA binding motif protein 11 C6orf225 chromosome 6 open reading frame 225 KIAA1984|C9orf86|TMEM14 1 KIAA1984 | chromosome 9 open reading frame 86 | transmembrane protein 141 KIAA1107 TLR3 toll-like receptor 3 LPAR6 lysophosphatidic acid receptor 6 KIAA1683 GRB10 growth factor receptor-bound protein 10 TIMP2 TIMP metallopeptidase inhibitor 2 CCDC28A coiled-coil domain containing 28A FBXL2 F-box and leucine-rich repeat protein 2 NOV nephroblastoma overexpressed gene TSPAN31 tetraspanin 31 NR3C2 nuclear receptor subfamily 3, group C, member 2 DYNC2LI1 dynein, cytoplasmic 2, light intermediate chain 1 C15orf51 dynamin 1 pseudogene SAMD13 sterile alpha motif domain containing 13 RASSF6 Ras association (RalGDS/AF-6) domain family member 6 ZNF167 zinc finger protein 167 GATA2 GATA binding protein 2 NUDT7 nudix (nucleoside diphosphate linked moiety X)-type motif 7 DNAJC18 DnaJ (Hsp40) homolog, subfamily C, member 18 SNORA57 small nucleolar RNA, H/ACA box 57 CALCOCO1 calcium binding and coiled-coil domain 1 RLN2 relaxin 2 ING4 inhibitor of growth family, member 4 NMT2 N-myristoyltransferase 2 ZNF512 zinc finger protein 512 YPEL5 yippee-like 5 (Drosophila) ANKRD31 ankyrin repeat domain 31 CSTT cystatin pseudogene EFCAB7 EF-hand calcium binding domain 7 FAM160A1 family with sequence similarity 160, member A1 PPM1N|FLJ40125 protein phosphatase, Mg2+/Mn2+ dependent, 1N (putative) | protein phosphatase 1B-like DENND5A DENN/MADD domain containing 5A RG9MTD3 RNA (guanine-9-) methyltransferase domain containing 3 SNORD104 small nucleolar RNA, C/D box 104 C20orf194 chromosome 20 open reading frame 194 PNRC1 proline-rich nuclear receptor coactivator 1 THSD1P1 thrombospondin, type I, domain containing 1 pseudogene 1 SGCB sarcoglycan, beta (43kDa dystrophin-associated glycoprotein) TMC5 transmembrane channel-like 5 ZNF10|ZNF268 zinc finger protein 10 | zinc finger protein 268 ARHGEF37|FLJ41603 Rho guanine nucleotide exchange factor (GEF) 37 | FLJ41603 protein KIDINS220 kinase D-interacting substrate, 220kDa BTG2 BTG family, member 2 LPIN1 lipin 1 PDZD4 PDZ domain containing 4 FCHSD1|RELL2 FCH and double SH3 domains 1 | RELT-like 2 DENND5B DENN/MADD domain containing 5B AMN1|C12orf72 antagonist of mitotic exit network 1 homolog (S. cerevisiae) | chromosome 12 open reading frame 72 ANKZF1 ankyrin repeat and zinc finger domain containing 1 RMND1 required for meiotic nuclear division 1 homolog (S. cerevisiae) FAM154B family with sequence similarity 154, member B C1orf61 chromosome 1 open reading frame 61 ATXN1 ataxin 1 SERPINA3 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 TBC1D19 TBC1 domain family, member 19 KLHL5 kelch-like 5 (Drosophila) thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) oncogene homolog, avian) | THRA|NR1D1 nuclear receptor subfamily 1, group D, member 1 H3F3B H3 histone, family 3B (H3.3B) NAALADL2 N-acetylated alpha-linked acidic dipeptidase-like 2 BTN2A2 butyrophilin, subfamily 2, member A2 CA13 carbonic anhydrase XIII FAM124A family with sequence similarity 124A C7orf41 chromosome 7 open reading frame 41 ATP6V1H ATPase, H+ transporting, lysosomal 50/57kDa, V1 subunit H CCL28 chemokine (C-C motif) ligand 28 C21orf57 chromosome 21 open reading frame 57 ZNF550 zinc finger protein 550 RASA4|RASA4P|RASA4B|P RAS p21 protein activator 4 | RAS p21 protein activator 4 pseudogene | RAS p21 protein activator OLR2J4|LOC100132214|LO 4B | polymerase (RNA) II (DNA directed) polypeptide J4, pseudogene | similar to calcium-promoted C100286937 Ras inactivator | similar to HSPC047 protein SPATA7 spermatogenesis associated 7 BCAS3 breast carcinoma amplified sequence 3 CASP8 caspase 8, apoptosis-related cysteine peptidase LCP1 lymphocyte cytosolic protein 1 (L-plastin) MMP26 matrix metallopeptidase 26 PAN2 PARP16 poly (ADP-ribose) polymerase family, member 16 GNB5 guanine nucleotide binding protein (G protein), beta 5 MYT1 myelin transcription factor 1 SLC12A6 solute carrier family 12 (potassium/chloride transporters), member 6 MEAF6 MYST/Esa1-associated factor 6 GPRC5B G protein-coupled receptor, family C, group 5, member B radial spoke head 10 homolog B (Chlamydomonas) | radial spoke head 10 homolog B2 RSPH10B|RSPH10B2 (Chlamydomonas) MCTS1 malignant T cell amplified sequence 1 RAS p21 protein activator 4 | RAS p21 protein activator 4 pseudogene | RAS p21 protein activator RASA4|RASA4P|RASA4B|P 4B | polymerase (RNA) II (DNA directed) polypeptide J4, pseudogene | similar to calcium-promoted OLR2J4|LOC100132214 Ras inactivator CD207 (MARCH8) membrane-associated ring finger (C3HC4) 8 RGL3 ral guanine nucleotide dissociation stimulator-like 3 radial spoke head 10 homolog B (Chlamydomonas) | radial spoke head 10 homolog B2 RSPH10B|RSPH10B2 (Chlamydomonas) SLC38A3 solute carrier family 38, member 3 SCN4B sodium channel, voltage-gated, type IV, beta C3orf17 chromosome 3 open reading frame 17 ABCA9 ATP-binding cassette, sub-family A (ABC1), member 9 SMYD2 SET and MYND domain containing 2 pleckstrin homology domain containing, family M (with RUN domain) member 1 pseudogene | similar PLEKHM1P|LOC100291232 to hCG2002091 C5orf32 chromosome 5 open reading frame 32 GPM6B glycoprotein M6B B9D1 B9 protein domain 1 PHKA2 phosphorylase kinase, alpha 2 (liver) OR1J2 olfactory receptor, family 1, subfamily J, member 2 NFATC1 nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1 SYNGR1 synaptogyrin 1 METTL6 methyltransferase like 6 OR56A4 olfactory receptor, family 56, subfamily A, member 4 ROPN1L ropporin 1-like APPL2 adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2 HSF2 heat shock transcription factor 2 RNF145 ring finger protein 145 NPHP1 nephronophthisis 1 (juvenile) complement component 4A (Rodgers blood group) | complement component 4B (Chido blood group) C4A|C4B|LOC100292046|L | similar to Complement component 4A (Rodgers blood group) | similar to complement component OC100294156 4A (Rodgers blood group) complement component 4A (Rodgers blood group) | complement component 4B (Chido blood group) C4A|C4B|LOC100292046|L | similar to Complement component 4A (Rodgers blood group) | similar to complement component OC100294156 4A (Rodgers blood group) CYP4F22 cytochrome P450, family 4, subfamily F, polypeptide 22 KIAA1704 PJA2 praja ring finger 2 C20orf90 chromosome 20 open reading frame 90 TMF1 TATA element modulatory factor 1 NEUROD4 neurogenic differentiation 4 SNX13 sorting nexin 13 DNAH12 dynein, axonemal, heavy chain 12 SEPSECS Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase C12orf76 chromosome 12 open reading frame 76 C3orf19|TMEM135 chromosome 3 open reading frame 19 | transmembrane protein 135 GJA5 gap junction protein, alpha 5, 40kDa SKP1 S-phase kinase-associated protein 1 RAB3GAP2 RAB3 GTPase activating protein subunit 2 (non-catalytic) HEMK1|C3orf18 HemK methyltransferase family member 1 | chromosome 3 open reading frame 18 RPS4Y1 ribosomal protein S4, Y-linked 1 ASB3|LOC100302652|GPR7 5 ankyrin repeat and SOCS box-containing 3 | GPR75-ASB3 | G protein-coupled receptor 75 CTBS chitobiase, di-N-acetyl- MLLT3 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 KCNIP2 Kv channel interacting protein 2 golgi-associated PDZ and coiled-coil motif containing | golgi associated PDZ and coiled-coil motif containing | discoidin, CUB and LCCL domain containing 1 | c-ros oncogene 1 , receptor tyrosine GOPC|DCBLD1|ROS1 kinase CCDC65 coiled-coil domain containing 65 VPS8 vacuolar protein sorting 8 homolog (S. cerevisiae) PHF21A PHD finger protein 21A OR5B2 olfactory receptor, family 5, subfamily B, member 2 FBXO24 F-box protein 24 NBR1 neighbor of BRCA1 gene 1 IL1F8 interleukin 1 family, member 8 (eta) NBAS neuroblastoma amplified sequence ZNF148 zinc finger protein 148 MIR206 microRNA 206 ARG1 arginase, liver TM4SF4 transmembrane 4 L six family member 4 RELB v-rel reticuloendotheliosis viral oncogene homolog B SH2D1B SH2 domain containing 1B DCP1B DCP1 decapping enzyme homolog B (S. cerevisiae) WDR33 WD repeat domain 33 MAPKAPK2 mitogen-activated protein kinase-activated protein kinase 2 SLC5A12 solute carrier family 5 (sodium/glucose cotransporter), member 12 Supplementary Table 2. List of genes down-regulated in abiraterone-resistant VCaP xenograft samples DPP4 dipeptidyl-peptidase 4 FAM189A2 family with sequence similarity 189, member A2 CENPE centromere protein E, 312kDa SGK3|C8orf44 serum/glucocorticoid regulated kinase family, member 3 | chromosome 8 open reading frame 44 OAS3 2'-5'-oligoadenylate synthetase 3, 100kDa MKI67 antigen identified by monoclonal antibody Ki-67 C15orf42 chromosome 15 open reading frame 42 ASPM asp (abnormal spindle) homolog, microcephaly associated (Drosophila) CDK1|CDC2 cyclin-dependent kinase 1 | cell division cycle 2, G1 to S and G2 to M NCAPG|LCORL non-SMC condensin I complex, subunit G | ligand dependent nuclear receptor corepressor-like LOC1720 dihydrofolate reductase pseudogene ARHGAP11A Rho GTPase activating protein 11A SHCBP1 SHC SH2-domain
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  • Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice

    Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice

    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia.
  • Supplementary Table 1: Adhesion Genes Data Set

    Supplementary Table 1: Adhesion Genes Data Set

    Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like,