Table of Contents

Total Page:16

File Type:pdf, Size:1020Kb

Table of Contents Table of Contents Comparison Page Numbers RF vs Static 2-231 HSS vs Static 232-507 LSS vs Static 508-715 RF vs HSS 716-746 RF vs LSS 747-751 HSS vs LSS 752-764 Fold change Regulation ([RF] vs ([RF] vs Probe Name [Static]) [Static]) Common name Gene Symbol Description Genbank Accession Homo sapiens apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B (APOBEC3B), A_24_P66027 2.741304 down NM_004900 APOBEC3B mRNA [NM_004900] NM_004900 Homo sapiens vasohibin 1 (VASH1), mRNA A_23_P77000 3.932838 down NM_014909 VASH1 [NM_014909] NM_014909 Homo sapiens transmembrane protein 97 A_24_P151920 2.292691 down NM_014573 TMEM97 (TMEM97), mRNA [NM_014573] NM_014573 CN479126 UI-CF-FN0-afv-i-22-0-UI.s1 UI-CF-FN0 Homo sapiens cDNA clone UI-CF-FN0-afv-i-22-0-UI A_32_P149011 3.661964 up CN479126 CN479126 3', mRNA sequence [CN479126] CN479126 Homo sapiens notchless homolog 1 (Drosophila) (NLE1), transcript variant 2, mRNA A_23_P141315 1.785076 down NM_001014445 NLE1 [NM_001014445] NM_001014445 Homo sapiens ribonucleotide reductase M1 A_23_P87351 1.519893 down NM_001033 RRM1 polypeptide (RRM1), mRNA [NM_001033] NM_001033 AT_ssH_PC_3 2.387579 down AT_ssH_PC_3 AT_ssH_PC_3 Homo sapiens huntingtin interacting protein 2 A_23_P155677 1.640733 up NM_005339 HIP2 (HIP2), mRNA [NM_005339] NM_005339 Homo sapiens chromosome 1 open reading frame A_24_P131173 3.527582 down NM_024709 C1orf115 115 (C1orf115), mRNA [NM_024709] NM_024709 Homo sapiens CCR4-NOT transcription complex, A_23_P110846 1.616577 up NM_004779 CNOT8 subunit 8 (CNOT8), mRNA [NM_004779] NM_004779 Homo sapiens protein kinase, AMP-activated, alpha A_23_P60811 3.629454 down NM_006252 PRKAA2 2 catalytic subunit (PRKAA2), mRNA [NM_006252] NM_006252 Homo sapiens pannexin 1 (PANX1), mRNA A_23_P47155 2.378446 up NM_015368 PANX1 [NM_015368] NM_015368 Homo sapiens chemokine (C-X-C motif) ligand 2 A_23_P315364 11.12551 down NM_002089 CXCL2 (CXCL2), mRNA [NM_002089] NM_002089 Centromere protein P (CENP-P). [Source:Uniprot/SWISSPROT;Acc:Q6IPU0] A_32_P93996 5.026525 down ENST00000375587 CENPP [ENST00000375587] Fold change Regulation ([RF] vs ([RF] vs Probe Name [Static]) [Static]) Common name Gene Symbol Description Genbank Accession Homo sapiens tumor necrosis factor, alpha-induced A_32_P59010 1.775864 up NM_207381 TNFAIP8L3 protein 8-like 3 (TNFAIP8L3), mRNA [NM_207381] NM_207381 Homo sapiens dynein, light chain, Tctex-type 3 A_24_P100368 3.098044 up NM_006520 DYNLT3 (DYNLT3), mRNA [NM_006520] NM_006520 Homo sapiens polymerase (DNA directed), epsilon A_23_P163099 3.5137 down NM_002692 POLE2 2 (p59 subunit) (POLE2), mRNA [NM_002692] NM_002692 Homo sapiens leucine rich repeat containing 4 A_23_P8625 12.80776 up NM_022143 LRRC4 (LRRC4), mRNA [NM_022143] NM_022143 Homo sapiens breast cancer 2, early onset A_23_P99452 4.193268 down NM_000059 BRCA2 (BRCA2), mRNA [NM_000059] NM_000059 Homo sapiens coiled-coil domain containing 92 A_23_P98900 1.608385 up NM_025140 CCDC92 (CCDC92), mRNA [NM_025140] NM_025140 Homo sapiens retrotransposon gag domain A_24_P289954 3.6215 up NM_001024455 RGAG4 containing 4 (RGAG4), mRNA [NM_001024455] NM_001024455 Homo sapiens aldehyde dehydrogenase 4 family, member A1 (ALDH4A1), nuclear gene encoding mitochondrial protein, transcript variant P5CDhL, A_23_P170337 2.541433 down NM_003748 ALDH4A1 mRNA [NM_003748] NM_003748 Homo sapiens SMAD family member 7 (SMAD7), A_23_P55518 18.66759 up NM_005904 SMAD7 mRNA [NM_005904] NM_005904 Homo sapiens nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) (NR3C1), A_23_P214059 3.292093 up NM_000176 NR3C1 transcript variant 5, mRNA [NM_000176] NM_000176 Homo sapiens SFT2 domain containing 1 A_23_P321959 1.932799 up NM_145169 SFT2D1 (SFT2D1), mRNA [NM_145169] NM_145169 Homo sapiens makorin, ring finger protein, 1 A_24_P29703 1.738564 up NM_013446 MKRN1 (MKRN1), mRNA [NM_013446] NM_013446 Homo sapiens complement component 1, r A_23_P125423 1.769302 down NM_001733 C1R subcomponent (C1R), mRNA [NM_001733] NM_001733 Fold change Regulation ([RF] vs ([RF] vs Probe Name [Static]) [Static]) Common name Gene Symbol Description Genbank Accession Homo sapiens matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV A_23_P163787 1.949149 up NM_004530 MMP2 collagenase) (MMP2), mRNA [NM_004530] NM_004530 Homo sapiens nischarin, mRNA (cDNA clone A_24_P925709 2.029638 up BC050552 NISCH IMAGE:5761683), partial cds. [BC050552] BC050552 Homo sapiens sulfotransferase family, cytosolic, 1A, phenol-preferring, member 2 (SULT1A2), transcript A_23_P106773 1.611623 up NM_177528 SULT1A2 variant 2, mRNA [NM_177528] NM_177528 Homo sapiens bromodomain adjacent to zinc finger domain, 1A (BAZ1A), transcript variant 1, mRNA A_23_P76799 1.509372 up NM_013448 BAZ1A [NM_013448] NM_013448 Homo sapiens ligand of numb-protein X 2 (LNX2), A_23_P402287 2.293423 up NM_153371 LNX2 mRNA [NM_153371] NM_153371 Homo sapiens KIAA0406 (KIAA0406), mRNA A_23_P109001 1.586107 down NM_014657 KIAA0406 [NM_014657] NM_014657 Homo sapiens ring finger protein 11 (RNF11), A_23_P137434 2.082176 up NM_014372 RNF11 mRNA [NM_014372] NM_014372 Homo sapiens serpin peptidase inhibitor, clade B (ovalbumin), member 8 (SERPINB8), transcript A_24_P147461 2.575153 up NM_198833 SERPINB8 variant 2, mRNA [NM_198833] NM_198833 Homo sapiens zinc finger protein 559 (ZNF559), A_24_P284584 1.501735 up NM_032497 ZNF559 mRNA [NM_032497] NM_032497 Homo sapiens zinc finger protein 697 (ZNF697), A_23_P322076 1.963568 up NM_001080470 ZNF697 mRNA [NM_001080470] NM_001080470 Homo sapiens tumor necrosis factor (ligand) superfamily, member 10 (TNFSF10), mRNA A_23_P121253 15.29152 down NM_003810 TNFSF10 [NM_003810] NM_003810 Homo sapiens cyclin A2 (CCNA2), mRNA A_23_P58321 6.913679 down NM_001237 CCNA2 [NM_001237] NM_001237 Homo sapiens lin-7 homolog B (C. elegans) A_23_P164912 5.903862 up NM_022165 LIN7B (LIN7B), mRNA [NM_022165] NM_022165 Homo sapiens tumor protein p53 inducible protein A_23_P150281 4.906311 down NM_001076787 TP53I11 11 (TP53I11), mRNA [NM_001076787] NM_001076787 Fold change Regulation ([RF] vs ([RF] vs Probe Name [Static]) [Static]) Common name Gene Symbol Description Genbank Accession Homo sapiens serine hydroxymethyltransferase 1 (soluble) (SHMT1), transcript variant 1, mRNA A_23_P502654 3.647096 down NM_004169 SHMT1 [NM_004169] NM_004169 Homo sapiens v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT), mRNA A_23_P110253 68.15226 down NM_000222 KIT [NM_000222] NM_000222 Homo sapiens ferritin, heavy polypeptide-like 12 A_24_P92771 3.085015 up NR_002205 FTHL12 (FTHL12) on chromosome 9 [NR_002205] NR_002205 Homo sapiens purinergic receptor P2X, ligand- A_23_P53623 3.181061 down NM_002560 P2RX4 gated ion channel, 4 (P2RX4), mRNA [NM_002560] NM_002560 Homo sapiens met proto-oncogene (hepatocyte A_23_P359245 3.913462 down NM_000245 MET growth factor receptor) (MET), mRNA [NM_000245] NM_000245 Homo sapiens CD40 molecule, TNF receptor superfamily member 5 (CD40), transcript variant 1, A_23_P57036 2.750283 down NM_001250 CD40 mRNA [NM_001250] NM_001250 Homo sapiens chromosome 10 open reading frame A_23_P35597 135.6612 down NM_007021 C10orf10 10 (C10orf10), mRNA [NM_007021] NM_007021 Homo sapiens muskelin 1, intracellular mediator containing kelch motifs (MKLN1), mRNA A_23_P93613 1.509905 up NM_013255 MKLN1 [NM_013255] NM_013255 Homo sapiens cDNA FLJ25640 fis, clone A_32_P226907 2.090486 down AK098506 LOC284112 STM04823. [AK098506] AK098506 Homo sapiens kinase suppressor of ras 2 (KSR2), A_32_P216635 6.771054 down NM_173598 KSR2 mRNA [NM_173598] NM_173598 Homo sapiens BTB and CNC homology 1, basic leucine zipper transcription factor 1 (BACH1), A_23_P211047 2.854582 up NM_206866 BACH1 transcript variant 1, mRNA [NM_206866] NM_206866 Homo sapiens zinc finger protein 419 (ZNF419), A_23_P164638 1.566116 up NM_024691 ZNF419 mRNA [NM_024691] NM_024691 Homo sapiens von Willebrand factor (VWF), mRNA A_23_P105562 2.424283 down NM_000552 VWF [NM_000552] NM_000552 Fold change Regulation ([RF] vs ([RF] vs Probe Name [Static]) [Static]) Common name Gene Symbol Description Genbank Accession Homo sapiens deoxyribonuclease I (DNASE1), A_23_P66311 1.790631 up NM_005223 DNASE1 mRNA [NM_005223] NM_005223 CD521096 AGENCOURT_14355292 NIH_MGC_191 Homo sapiens cDNA clone A_32_P69136 2.174208 down THC2739760 THC2739760 IMAGE:30410815 5', mRNA sequence [CD521096] Homo sapiens cDNA FLJ27513 fis, clone A_24_P467073 6.629169 up AK131023 AK131023 TST08509. [AK131023] AK131023 Homo sapiens diacylglycerol O-acyltransferase A_23_P53198 6.820694 down NM_032564 DGAT2 homolog 2 (mouse) (DGAT2), mRNA [NM_032564] NM_032564 Interleukin-6 receptor subunit beta precursor (IL-6R- beta) (Interleukin-6 signal transducer) (Membrane glycoprotein 130) (gp130) (Oncostatin-M receptor alpha subunit) (CD130 antigen) (CDw130). [Source:Uniprot/SWISSPROT;Acc:P40189] A_32_P223777 2.072202 up ENST00000381298 ENST00000381298 [ENST00000381298] Homo sapiens Fanconi anemia, complementation group A (FANCA), transcript variant 1, mRNA A_23_P206441 4.266227 down NM_000135 FANCA [NM_000135] NM_000135 Homo sapiens solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 A_23_P255837 8.369516 up NM_003046 SLC7A2 (SLC7A2), transcript variant 1, mRNA [NM_003046] NM_003046 A_24_P32715 5.543256 up A_24_P32715 A_24_P32715 Homo sapiens SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae) (SPC25), A_23_P51085 6.778013 down NM_020675 SPC25 mRNA [NM_020675] NM_020675 Homo sapiens exonuclease 1 (EXO1), transcript A_23_P23303 2.239646 down NM_003686 EXO1 variant 3, mRNA [NM_003686] NM_003686
Recommended publications
  • Supplementary Information
    doi: 10.1038/nature08795 SUPPLEMENTARY INFORMATION Supplementary Discussion Population naming In some contexts, the indigenous hunter-gatherer and pastoralist peoples of southern Africa are referred to collectively as the Khoisan (Khoi-San) or more recently Khoesan (Khoe-San) people. This grouping is based on the unique linguistic use of click-consonants1. Many names, often country-specific, have been used by Bantu pastoralists and European settlers to describe the hunter-gatherers, including San, Saan, Sonqua, Soaqua, Souqua, Sanqua, Kwankhala, Basarwa, Batwa, Abathwa, Baroa, Bushmen, Bossiesmans, Bosjemans, or Bosquimanos. In addition, group-specific names such as !Kung and Khwe are often used for the broader population. The two most commonly used names, “San” and “Bushmen”, have both been associated with much controversy due to derogatory connotations2. “San” has become the more popular term used in Western literature, although “Bushmen” is arguably the more commonly recognized term within the communities. Since they have no collective name for themselves, the term Bushmen was selected for use in this paper as the term most familiar to the participants themselves. Regarding identification of individuals The five men identified in this study have all elected to have their identity made public knowledge. Thus we present two complete personal genomes (KB1 and ABT), a low-coverage personal genome (NB1), and personal exomes for all five men. On a scientific level, identification allows for current and future correlation of genetic data with demographic and medical histories. On a social level, identification allows for maximizing community benefit. For !Gubi, G/aq’o, D#kgao and !Aî, their name represents not only themselves, but importantly their extended family unit and a way of life severely under threat.
    [Show full text]
  • Nuclear and Mitochondrial Genome Defects in Autisms
    UC Irvine UC Irvine Previously Published Works Title Nuclear and mitochondrial genome defects in autisms. Permalink https://escholarship.org/uc/item/8vq3278q Journal Annals of the New York Academy of Sciences, 1151(1) ISSN 0077-8923 Authors Smith, Moyra Spence, M Anne Flodman, Pamela Publication Date 2009 DOI 10.1111/j.1749-6632.2008.03571.x License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California THE YEAR IN HUMAN AND MEDICAL GENETICS 2009 Nuclear and Mitochondrial Genome Defects in Autisms Moyra Smith, M. Anne Spence, and Pamela Flodman Department of Pediatrics, University of California, Irvine, California In this review we will evaluate evidence that altered gene dosage and structure im- pacts neurodevelopment and neural connectivity through deleterious effects on synap- tic structure and function, and evidence that the latter are key contributors to the risk for autism. We will review information on alterations of structure of mitochondrial DNA and abnormal mitochondrial function in autism and indications that interactions of the nuclear and mitochondrial genomes may play a role in autism pathogenesis. In a final section we will present data derived using Affymetrixtm SNP 6.0 microar- ray analysis of DNA of a number of subjects and parents recruited to our autism spectrum disorders project. We include data on two sets of monozygotic twins. Col- lectively these data provide additional evidence of nuclear and mitochondrial genome imbalance in autism and evidence of specific candidate genes in autism. We present data on dosage changes in genes that map on the X chromosomes and the Y chro- mosome.
    [Show full text]
  • ALS2CR2 (STRADB) 406-418) Goat Polyclonal Antibody – AP08962PU-N
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for AP08962PU-N ALS2CR2 (STRADB) 406-418) Goat Polyclonal Antibody Product data: Product Type: Primary Antibodies Applications: ELISA, IHC, WB Recommended Dilution: ELISA: 1/32000. Immunohistochemistry on Paraffin Sections: 3.75 µg/ml. Western Blot: 1 - 3 µg/ml. Reactivity: Canine, Human Host: Goat Clonality: Polyclonal Immunogen: Synthetic peptide from C-terminus of human ALS2CR2 Specificity: This antibody reacts to STE20-Related Kinase Adaptor Beta (STRADB/ALS2CR2) at aa 406-418. It is expected to recognise both human isoforms: ILPIP-alpha (NP_061041.2) and ILPIP-beta (AAF71042.1). Formulation: Tris saline buffer, pH 7.3, 0.5% BSA, 0.02% sodium azide State: Aff - Purified State: Liquid purified Ig Concentration: lot specific Purification: Immunoaffinity Chromatography Conjugation: Unconjugated Storage: Store the antibody undiluted at 2-8°C for one month or (in aliquots) at -20°C for longer. Avoid repeated freezing and thawing. Stability: Shelf life: one year from despatch. Database Link: Entrez Gene 55437 Human Q9C0K7 This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 3 ALS2CR2 (STRADB) 406-418) Goat Polyclonal Antibody – AP08962PU-N Background: Amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2, is connected to transferase/kinase activity and ATP binding, it has recently been shown to interact with XIAP, a member of the IAP (Inhibitor of Apoptosis) protein family.
    [Show full text]
  • Bayesian Hierarchical Modeling of High-Throughput Genomic Data with Applications to Cancer Bioinformatics and Stem Cell Differentiation
    BAYESIAN HIERARCHICAL MODELING OF HIGH-THROUGHPUT GENOMIC DATA WITH APPLICATIONS TO CANCER BIOINFORMATICS AND STEM CELL DIFFERENTIATION by Keegan D. Korthauer A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Statistics) at the UNIVERSITY OF WISCONSIN–MADISON 2015 Date of final oral examination: 05/04/15 The dissertation is approved by the following members of the Final Oral Committee: Christina Kendziorski, Professor, Biostatistics and Medical Informatics Michael A. Newton, Professor, Statistics Sunduz Kele¸s,Professor, Biostatistics and Medical Informatics Sijian Wang, Associate Professor, Biostatistics and Medical Informatics Michael N. Gould, Professor, Oncology © Copyright by Keegan D. Korthauer 2015 All Rights Reserved i in memory of my grandparents Ma and Pa FL Grandma and John ii ACKNOWLEDGMENTS First and foremost, I am deeply grateful to my thesis advisor Christina Kendziorski for her invaluable advice, enthusiastic support, and unending patience throughout my time at UW-Madison. She has provided sound wisdom on everything from methodological principles to the intricacies of academic research. I especially appreciate that she has always encouraged me to eke out my own path and I attribute a great deal of credit to her for the successes I have achieved thus far. I also owe special thanks to my committee member Professor Michael Newton, who guided me through one of my first collaborative research experiences and has continued to provide key advice on my thesis research. I am also indebted to the other members of my thesis committee, Professor Sunduz Kele¸s,Professor Sijian Wang, and Professor Michael Gould, whose valuable comments, questions, and suggestions have greatly improved this dissertation.
    [Show full text]
  • AGAP1 (NM 014914) Human Recombinant Protein Product Data
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TP314836 AGAP1 (NM_014914) Human Recombinant Protein Product data: Product Type: Recombinant Proteins Description: Recombinant protein of human ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 (AGAP1), transcript variant 2 Species: Human Expression Host: HEK293T Tag: C-Myc/DDK Predicted MW: 88.9 kDa Concentration: >50 ug/mL as determined by microplate BCA method Purity: > 80% as determined by SDS-PAGE and Coomassie blue staining Buffer: 25 mM Tris.HCl, pH 7.3, 100 mM glycine, 10% glycerol Preparation: Recombinant protein was captured through anti-DDK affinity column followed by conventional chromatography steps. Storage: Store at -80°C. Stability: Stable for 12 months from the date of receipt of the product under proper storage and handling conditions. Avoid repeated freeze-thaw cycles. RefSeq: NP_055729 Locus ID: 116987 UniProt ID: Q9UPQ3 RefSeq Size: 4078 Cytogenetics: 2q37.2 RefSeq ORF: 2412 Synonyms: AGAP-1; CENTG2; cnt-g2; GGAP1 Summary: This gene encodes a member of an ADP-ribosylation factor GTPase-activating protein family involved in membrane trafficking and cytoskeleton dynamics. This gene functions as a direct regulator of the adaptor-related protein complex 3 on endosomes. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011] This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 AGAP1 (NM_014914) Human Recombinant Protein – TP314836 Protein Pathways: Endocytosis Product images: Coomassie blue staining of purified AGAP1 protein (Cat# TP314836).
    [Show full text]
  • Human ADAM12 Quantikine ELISA
    Quantikine® ELISA Human ADAM12 Immunoassay Catalog Number DAD120 For the quantitative determination of A Disintegrin And Metalloproteinase domain- containing protein 12 (ADAM12) concentrations in cell culture supernates, serum, plasma, and urine. This package insert must be read in its entirety before using this product. For research use only. Not for use in diagnostic procedures. TABLE OF CONTENTS SECTION PAGE INTRODUCTION .....................................................................................................................................................................1 PRINCIPLE OF THE ASSAY ...................................................................................................................................................2 LIMITATIONS OF THE PROCEDURE .................................................................................................................................2 TECHNICAL HINTS .................................................................................................................................................................2 MATERIALS PROVIDED & STORAGE CONDITIONS ...................................................................................................3 OTHER SUPPLIES REQUIRED .............................................................................................................................................3 PRECAUTIONS .........................................................................................................................................................................4
    [Show full text]
  • Further Delineation of Chromosomal Consensus Regions in Primary
    Leukemia (2007) 21, 2463–2469 & 2007 Nature Publishing Group All rights reserved 0887-6924/07 $30.00 www.nature.com/leu ORIGINAL ARTICLE Further delineation of chromosomal consensus regions in primary mediastinal B-cell lymphomas: an analysis of 37 tumor samples using high-resolution genomic profiling (array-CGH) S Wessendorf1,6, TFE Barth2,6, A Viardot1, A Mueller3, HA Kestler3, H Kohlhammer1, P Lichter4, M Bentz5,HDo¨hner1,PMo¨ller2 and C Schwaenen1 1Klinik fu¨r Innere Medizin III, Zentrum fu¨r Innere Medizin der Universita¨t Ulm, Ulm, Germany; 2Institut fu¨r Pathologie, Universita¨t Ulm, Ulm, Germany; 3Forschungsdozentur Bioinformatik, Universita¨t Ulm, Ulm, Germany; 4Abt. Molekulare Genetik, Deutsches Krebsforschungszentrum, Heidelberg, Germany and 5Sta¨dtisches Klinikum Karlsruhe, Karlsruhe, Germany Primary mediastinal B-cell lymphoma (PMBL) is an aggressive the expression of BSAP, BOB1, OCT2, PAX5 and PU1 was extranodal B-cell non-Hodgkin’s lymphoma with specific clin- added to the spectrum typical of PMBL features.9 ical, histopathological and genomic features. To characterize Genetically, a pattern of highly recurrent karyotype alterations further the genotype of PMBL, we analyzed 37 tumor samples and PMBL cell lines Med-B1 and Karpas1106P using array- with the hallmark of chromosomal gains of the subtelomeric based comparative genomic hybridization (matrix- or array- region of chromosome 9 supported the concept of a unique CGH) to a 2.8k genomic microarray. Due to a higher genomic disease entity that distinguishes PMBL from other B-cell non- resolution, we identified altered chromosomal regions in much Hodgkin’s lymphomas.10,11 Together with less specific gains on higher frequencies compared with standard CGH: for example, 2p15 and frequent mutations of the SOCS1 gene, a notable þ 9p24 (68%), þ 2p15 (51%), þ 7q22 (32%), þ 9q34 (32%), genomic similarity to classical Hodgkin’s lymphoma was þ 11q23 (18%), þ 12q (30%) and þ 18q21 (24%).
    [Show full text]
  • Supplemental Table S1
    Entrez Gene Symbol Gene Name Affymetrix EST Glomchip SAGE Stanford Literature HPA confirmed Gene ID Profiling profiling Profiling Profiling array profiling confirmed 1 2 A2M alpha-2-macroglobulin 0 0 0 1 0 2 10347 ABCA7 ATP-binding cassette, sub-family A (ABC1), member 7 1 0 0 0 0 3 10350 ABCA9 ATP-binding cassette, sub-family A (ABC1), member 9 1 0 0 0 0 4 10057 ABCC5 ATP-binding cassette, sub-family C (CFTR/MRP), member 5 1 0 0 0 0 5 10060 ABCC9 ATP-binding cassette, sub-family C (CFTR/MRP), member 9 1 0 0 0 0 6 79575 ABHD8 abhydrolase domain containing 8 1 0 0 0 0 7 51225 ABI3 ABI gene family, member 3 1 0 1 0 0 8 29 ABR active BCR-related gene 1 0 0 0 0 9 25841 ABTB2 ankyrin repeat and BTB (POZ) domain containing 2 1 0 1 0 0 10 30 ACAA1 acetyl-Coenzyme A acyltransferase 1 (peroxisomal 3-oxoacyl-Coenzyme A thiol 0 1 0 0 0 11 43 ACHE acetylcholinesterase (Yt blood group) 1 0 0 0 0 12 58 ACTA1 actin, alpha 1, skeletal muscle 0 1 0 0 0 13 60 ACTB actin, beta 01000 1 14 71 ACTG1 actin, gamma 1 0 1 0 0 0 15 81 ACTN4 actinin, alpha 4 0 0 1 1 1 10700177 16 10096 ACTR3 ARP3 actin-related protein 3 homolog (yeast) 0 1 0 0 0 17 94 ACVRL1 activin A receptor type II-like 1 1 0 1 0 0 18 8038 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 1 0 0 0 0 19 8751 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 1 0 0 0 0 20 8728 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 1 0 0 0 0 21 81792 ADAMTS12 ADAM metallopeptidase with thrombospondin type 1 motif, 12 1 0 0 0 0 22 9507 ADAMTS4 ADAM metallopeptidase with thrombospondin type 1
    [Show full text]
  • Quantikine® ELISA
    Quantikine® ELISA Human ADAMTS13 Immunoassay Catalog Number DADT130 For the quantitative determination of human A Disintegrin And Metalloproteinase with Thombospondin type 1 motif, 13 (ADAMTS13) concentrations in cell culture supernates, serum, and plasma. This package insert must be read in its entirety before using this product. For research use only. Not for use in diagnostic procedures. TABLE OF CONTENTS SECTION PAGE INTRODUCTION .....................................................................................................................................................................1 PRINCIPLE OF THE ASSAY ...................................................................................................................................................2 LIMITATIONS OF THE PROCEDURE .................................................................................................................................2 TECHNICAL HINTS .................................................................................................................................................................2 MATERIALS PROVIDED & STORAGE CONDITIONS ...................................................................................................3 OTHER SUPPLIES REQUIRED .............................................................................................................................................4 PRECAUTIONS .........................................................................................................................................................................4
    [Show full text]
  • Meta-Analyses of Expression Profiling Data in the Postmortem
    META-ANALYSES OF EXPRESSION PROFILING DATA IN THE POSTMORTEM HUMAN BRAIN by Meeta Mistry B.Sc., McMaster University, 2005 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES (Bioinformatics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) July 2012 © Meeta Mistry, 2012 Abstract Schizophrenia is a severe psychiatric illness for which the precise etiology remains unknown. Studies using postmortem human brain have become increasingly important in schizophrenia research, providing an opportunity to directly investigate the diseased brain tissue. Gene expression profiling technologies have been used by a number of groups to explore the postmortem human brain and seek genes which show changes in expression correlated with schizophrenia. While this has been a valuable means of generating hypotheses, there is a general lack of consensus in the findings across studies. Expression profiling of postmortem human brain tissue is difficult due to the effect of various factors that can confound the data. The first aim of this thesis was to use control postmortem human cortex for identification of expression changes associated with several factors, specifically: age, sex, brain pH and postmortem interval. I conducted a meta-analysis across the control arm of eleven microarray datasets (representing over 400 subjects), and identified a signature of genes associated with each factor. These genes provide critical information towards the identification of problematic genes when investigating postmortem human brain in schizophrenia and other neuropsychiatric illnesses. The second aim of this thesis was to evaluate gene expression patterns in the prefrontal cortex associated with schizophrenia by exploring two methods of analysis: differential expression and coexpression.
    [Show full text]
  • Targeted Resequencing Identifies Genes with Recurrent Variation In
    www.nature.com/npjgenmed ARTICLE OPEN Targeted resequencing identifies genes with recurrent variation in cerebral palsy C. L. van Eyk 1,2, M. A. Corbett 1,2, M. S. B. Frank 1,2, D. L. Webber1,2, M. Newman3, J. G. Berry 1,2, K. Harper1,2, B. P. Haines1,2, G. McMichael1,2, J. A. Woenig1,2, A. H. MacLennan1,2 and J. Gecz 1,2,4* A growing body of evidence points to a considerable and heterogeneous genetic aetiology of cerebral palsy (CP). To identify recurrently variant CP genes, we designed a custom gene panel of 112 candidate genes. We tested 366 clinically unselected singleton cases with CP, including 271 cases not previously examined using next-generation sequencing technologies. Overall, 5.2% of the naïve cases (14/271) harboured a genetic variant of clinical significance in a known disease gene, with a further 4.8% of individuals (13/271) having a variant in a candidate gene classified as intolerant to variation. In the aggregate cohort of individuals from this study and our previous genomic investigations, six recurrently hit genes contributed at least 4% of disease burden to CP: COL4A1, TUBA1A, AGAP1, L1CAM, MAOB and KIF1A. Significance of Rare VAriants (SORVA) burden analysis identified four genes with a genome-wide significant burden of variants, AGAP1, ERLIN1, ZDHHC9 and PROC, of which we functionally assessed AGAP1 using a zebrafish model. Our investigations reinforce that CP is a heterogeneous neurodevelopmental disorder with known as well as novel genetic determinants. npj Genomic Medicine (2019) ; https://doi.org/10.1038/s41525-019-0101-z4:27 1234567890():,; INTRODUCTION is likely also due in part to the stringent criteria used to select Cerebral palsy (CP) is the most common motor disability of causative variants.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2012/0264.634 A1 Amersdorfer Et Al
    US 20120264.634A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0264.634 A1 Amersdorfer et al. (43) Pub. Date: Oct. 18, 2012 (54) MARKER SEQUENCES FOR PANCREATIC Publication Classification CANCER DISEASES, PANCREATIC (51) Int. Cl. CARCINOMIA AND USE THEREOF C40B 30/04 (2006.01) GOIN 2L/64 (2006.01) (75) Inventors: Peter Amersdorfer, Graz (AT); GOIN 27/72 (2006.01) Annabel Höpfner, Dortmund (DE); C07K I4/435 (2006.01) Angelika Lueking, Bochum (DE) C40B 40/06 (2006.01) C40B 40/10 (2006.01) CI2N 5/09 (2010.01) (73) Assignee: PROTAGEN Aktiengesellschaft, C7H 2L/04 (2006.01) Dortmund (DE) GOIN 33/574 (2006.01) GOIN 27/62 (2006.01) (21) Appl. No.: 13/498,964 (52) U.S. Cl. ........... 506/9:436/501; 435/6.14; 435/7.92; 506/16:506/18: 435/2:536/23.1; 530/350 (22) PCT Filed: Sep. 29, 2010 (57) ABSTRACT The present invention relates to novel marker sequences for (86). PCT No.: PCT/EP2010/064510 pancreatic cancer diseases, pancreatic carcinoma and the diagnostic use thereof together with a method for Screening of S371 (c)(1), potential active Substances for pancreatic cancer diseases, (2), (4) Date: Jun. 22, 2012 pancreatic carcinoma by means of these marker sequences. Furthermore, the invention relates to a diagnostic device con (30) Foreign Application Priority Data taining Such marker sequences for pancreatic cancer diseases, pancreatic carcinoma, in particular a protein biochip and the Sep. 29, 2009 (EP) .................................. O9171690.2 use thereof. Patent Application Publication Oct. 18, 2012 US 2012/0264.634 A1 US 2012/0264.634 A1 Oct.
    [Show full text]