An Online Tool for Correlation and Functional Enrichment of Proteome-Wide Systems Genetics
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Frequent Expression Loss of Inter-Alpha-Trypsin Inhibitor Heavy Chain (ITIH) Genes in Multiple Human Solid Tumors: a Systematic Expression Analysis
Hamm, A; Veeck, J; Bektas, N; Wild, P J; Hartmann, A; Heindrichs, U; Kristiansen, G; Werbowetski-Ogilvie, T; Del Maestro, R; Knuechel, R; Dahl, E (2008). Frequent expression loss of Inter-alpha-trypsin inhibitor heavy chain (ITIH) genes in multiple human solid tumors: a systematic expression analysis. BMC Cancer, 8:25. Postprint available at: http://www.zora.uzh.ch University of Zurich Posted at the Zurich Open Repository and Archive, University of Zurich. Zurich Open Repository and Archive http://www.zora.uzh.ch Originally published at: BMC Cancer 2008, 8:25. Winterthurerstr. 190 CH-8057 Zurich http://www.zora.uzh.ch Year: 2008 Frequent expression loss of Inter-alpha-trypsin inhibitor heavy chain (ITIH) genes in multiple human solid tumors: a systematic expression analysis Hamm, A; Veeck, J; Bektas, N; Wild, P J; Hartmann, A; Heindrichs, U; Kristiansen, G; Werbowetski-Ogilvie, T; Del Maestro, R; Knuechel, R; Dahl, E Hamm, A; Veeck, J; Bektas, N; Wild, P J; Hartmann, A; Heindrichs, U; Kristiansen, G; Werbowetski-Ogilvie, T; Del Maestro, R; Knuechel, R; Dahl, E (2008). Frequent expression loss of Inter-alpha-trypsin inhibitor heavy chain (ITIH) genes in multiple human solid tumors: a systematic expression analysis. BMC Cancer, 8:25. Postprint available at: http://www.zora.uzh.ch Posted at the Zurich Open Repository and Archive, University of Zurich. http://www.zora.uzh.ch Originally published at: BMC Cancer 2008, 8:25. Frequent expression loss of Inter-alpha-trypsin inhibitor heavy chain (ITIH) genes in multiple human solid tumors: a systematic expression analysis Abstract BACKGROUND: The inter-alpha-trypsin inhibitors (ITI) are a family of plasma protease inhibitors, assembled from a light chain - bikunin, encoded by AMBP - and five homologous heavy chains (encoded by ITIH1, ITIH2, ITIH3, ITIH4, and ITIH5), contributing to extracellular matrix stability by covalent linkage to hyaluronan. -
(WCPG): Poster Abstracts: Sunday
ARTICLE IN PRESS JID: NEUPSY [m6+; October 2, 2018;12:59 ] European Neuropsychopharmacology (2018) 000, 1–75 www.elsevier.com/locate/euroneuro Abstracts of the 26th World Congress of Psychiatric Genetics (WCPG): Poster Abstracts: Sunday Sunday, October 14, 2018 with a 2kb upstream and 1kb downstream region was consid- ered for each gene. Gene-set analysis was conducted using MAGMA, with a principal components regression model for gene-based analyses. Sex, age, the 10 first and otherwise as- Poster Session III sociated principal components were included as covariates 4:00 p.m. - 6:00 p.m. in this step. We retrieved a “Hallmark Androgen response” gene-set from MSigDB to be tested in a case-control asso- SU1 ciation study. This gene-set contains 98 curated genes in- ANDROGEN RECEPTOR SIGNALING PATHWAYS IN- volved in the response to androgen receptor signaling. Also, FLUENCE IN ATTENTION-DEFICIT/HYPERACTIVITY a list of 534 annotated genes with at least one occurrence DISORDER of potential transcription factor binding sites (TFBS) for AR was created to investigate potential gene targets related to Djenifer Kappel 1, Bruna da Silva 1, Renata B. Cupertino 1, ADHD susceptibility. Diana Müller 1, Vitor Breda 2, Stefania Pigatto Teche 2, Results: No genome-wide association was observed at the Rogério Margis 1, Luis Augusto Rohde 2, Nina Roth Mota 3, SNPs or gene level. In the gene-set analysis, we found evi- Diego L. Rovaris 1, Eugênio H. Grevet 1, Claiton Bau 1 dence that the “Hallmark Androgen response” gene-set was significantly associated with ADHD susceptibility in our sam- 1 Universidade Federal do Rio Grande do Sul ple (p = 0.039). -
WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T (51) International Patent Classification: David [US/US]; 13539 N . 95th Way, Scottsdale, AZ C12Q 1/68 (2006.01) 85260 (US). (21) International Application Number: (74) Agent: AKHAVAN, Ramin; Caris Science, Inc., 6655 N . PCT/US20 12/0425 19 Macarthur Blvd., Irving, TX 75039 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 14 June 2012 (14.06.2012) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, English (25) Filing Language: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, Publication Language: English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/497,895 16 June 201 1 (16.06.201 1) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/499,138 20 June 201 1 (20.06.201 1) US OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, SD, 61/501,680 27 June 201 1 (27.06.201 1) u s SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, 61/506,019 8 July 201 1(08.07.201 1) u s TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
Genetic Associations with Cognitive Performance in Psychotic Disorders from the Bipolar-Schizophrenia Network on Intermediate Phenotypes Consortium Jeffrey R
Genetic associations with cognitive performance in psychotic disorders from the Bipolar-Schizophrenia Network on Intermediate Phenotypes consortium Jeffrey R. Bishop1, Lauren J. Mills1, S. Kristian Hill2, Ney Alliey-Rodriguez3, James L. Reilly4, Pranav Nanda5, Jaya Padmanabhan5, Neeraj Tandon6, Rebecca Shafee7, Steve McCarroll7, Steven Hyman7, Richard S.E. Keefe8, Godfrey D. Pearlson9, Brett A. Clementz10, Carol A. Tamminga11, Matcheri S. Keshavan5, Elliot S. Gershon3, John A. Sweeney12 1. University of Minnesota; 2. Rosalind Franklin University; 3. University of Chicago; 4. Northwestern University; 5. Harvard University; 6. Baylor University; 7. The Broad Institute; 8. Duke University; 9. Yale University; 10. University of Georgia; 11. University of Texas-Southwestern; 12. University of Cincinnati Abstract Genome-wide association study of BACS performance Background: Cognitive deficits are known to be present and familial in schizophrenia and bipolar disorder. Understanding the Caucasian Ancestry genetic contributors to cognitive impairments in psychotic disorders as well as healthy controls can contribute to our understanding of disease pathophysiology and its behavioral consequences. Chr3: SFMBT1 – related to expression factors Methods: The Brief Assessment of Cognition in Schizophrenia (BACS) was administered to 1059 participants (schizophrenia related to histone and chromatin regulation. N=299, schizoaffective disorder N=179, psychotic bipolar disorder N=236, and controls N=345) in the Bipolar-Schizophrenia Network on Intermediate Phenotypes (B-SNIP) study. Participants were 15-65 years of age, clinically stable outpatients (if p=2.410E-7 probands), and without significant neurological disorder, or recent substance abuse or dependence. Participants were genotyped using the Illumina PsychChip followed by imputation using the 1000Genomes reference panel resulting in 4,322,238 SNP markers. -
Candidate Chromosome 1 Disease Susceptibility Genes for Sjogren's Syndrome Xerostomia Are Narrowed by Novel NOD.B10 Congenic Mice P
Donald and Barbara Zucker School of Medicine Journal Articles Academic Works 2014 Candidate chromosome 1 disease susceptibility genes for Sjogren's syndrome xerostomia are narrowed by novel NOD.B10 congenic mice P. K. A. Mongini Zucker School of Medicine at Hofstra/Northwell J. M. Kramer Northwell Health T. Ishikawa H. Herschman D. Esposito Follow this and additional works at: https://academicworks.medicine.hofstra.edu/articles Part of the Medical Molecular Biology Commons Recommended Citation Mongini P, Kramer J, Ishikawa T, Herschman H, Esposito D. Candidate chromosome 1 disease susceptibility genes for Sjogren's syndrome xerostomia are narrowed by novel NOD.B10 congenic mice. 2014 Jan 01; 153(1):Article 2861 [ p.]. Available from: https://academicworks.medicine.hofstra.edu/articles/2861. Free full text article. This Article is brought to you for free and open access by Donald and Barbara Zucker School of Medicine Academic Works. It has been accepted for inclusion in Journal Articles by an authorized administrator of Donald and Barbara Zucker School of Medicine Academic Works. For more information, please contact [email protected]. NIH Public Access Author Manuscript Clin Immunol. Author manuscript; available in PMC 2015 July 01. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Clin Immunol. 2014 July ; 153(1): 79–90. doi:10.1016/j.clim.2014.03.012. Candidate chromosome 1 disease susceptibility genes for Sjogren’s syndrome xerostomia are narrowed by novel NOD.B10 congenic mice Patricia K. A. Monginia and Jill M. Kramera,1 Tomo-o Ishikawab,2 and Harvey Herschmanb Donna Espositoc aThe Feinstein Institute for Medical Research North Shore-Long Island Jewish Health System 350 Community Drive Manhasset, NY 11030 bDavid Geffen School of Medicine at UCLA 341 Boyer Hall (MBI) 611 Charles E. -
Pancreatic Progenitor Cells in Mice
PANCREATIC PROGENITOR CELLS IN MICE by Megan Hussey Cleveland A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2014 Abstract We generated a novel transgenic mouse expressing a tdTomato fluorophore, as well as a Strep/Flag-tagged version of Ptf1a from the native Ptf1a locus. I crossed this mouse line with the well-characterized Pdx1-GFP mouse, which enabled us to visualize and sort for cells of the “tip” and “trunk” progenitor domains of the mouse pancreas. The main goal of our project was to identify previously unrecognized early transcriptional targets of Ptf1at and Pdx1. I isolated early E11.5 epithelial progenitors as well as later E13.5 tip and trunk progenitors using FACS and analyzed these populations via the GeneChip Mouse Gene 1.0 ST Array. After comparison of microarray data between tip and trunk cells, differentially- expressed genes were identified, with a focus on transcription factors, with validation by in situ hybridization. Two transcription factors, Ascl2 and Lhx1, were initially identified that had no previously known role in pancreas development, and were shown by ISH to be expressed in the expected domain of the pancreas. I performed prelimary functional studies on these two transcription factors, using lentiviral shRNAs for knock down in dorsal pancreatic bud culture. ii Acknowledgments First, I would like to thank Steven Leach for accepting me into his lab and for the 7 years of mentorship he has provided. I would like to thank Sandy Muscelli, Dave Valle, Kirby Smith, Andy McCallion and the rest of the Human Genetics department for giving me the opportunity to pursue my Ph.D. -
Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus Dromedarius
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications from the Department of Electrical & Computer Engineering, Department Electrical and Computer Engineering of 2009 Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius Abdulaziz M. Al-Swailem King Abdulaziz City for Science and Technology Maher M. Shehata King Abdulaziz City for Science and Technology Faisel M. Abu-Duhier King Abdulaziz City for Science and Technology Essam J. Al-Yamani King Abdulaziz City for Science and Technology Khalid A. Al-Busadah King Faisal University See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/electricalengineeringfacpub Part of the Computer Engineering Commons, and the Electrical and Computer Engineering Commons Al-Swailem, Abdulaziz M.; Shehata, Maher M.; Abu-Duhier, Faisel M.; Al-Yamani, Essam J.; Al-Busadah, Khalid A.; Al-Arawi, Mohammed S.; Al-Khider, Ali Y.; Al-Muhaimeed, Abdullah N.; Al-Qahtani, Fahad H.; Manee, Manee M.; Al-Shomrani, Badr M.; Al-Qhtani, Saad M.; Al-Harthi, Amer S.; Akdemir, Kadir C.; Inan, Mehmet S.; and Otu, Hasan H., "Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius" (2009). Faculty Publications from the Department of Electrical and Computer Engineering. 426. https://digitalcommons.unl.edu/electricalengineeringfacpub/426 This Article is brought to you for free and open access by the Electrical & Computer Engineering, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications from the Department of Electrical and Computer Engineering by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Abdulaziz M. Al-Swailem, Maher M. -
Epigenetic Element-Based Transcriptome-Wide Association Study Identifies
medRxiv preprint doi: https://doi.org/10.1101/2020.07.23.20161174; this version posted August 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Epigenetic Element-Based Transcriptome-Wide Association Study Identifies Novel Genes for Bipolar Disorder Shi Yao1, Jing-Miao Ding1, Hao Wu1, Ruo-Han Hao1, Yu Rong1, Xin Ke1, Jing Guo1, Shan-Shan Dong1, Yan Guo1 1Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China, 710049 *Corresponding authors: Yan Guo, Ph.D. PHONE: 86-29-62818386 E-MAIL: [email protected] Running title: ETWAS for Bipolar Disorder NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.07.23.20161174; this version posted August 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Bipolar disorder (BD) is a highly heritable neuropsychiatric disorder characterized by recurrent episodes of depression and mania. Since the signals identified by genome-wide association study (GWAS) often reside in the non-coding regions, understanding the biological relevance of these genetic loci has proven to be complicated. -
Identification, by Systematic RNA Sequencing, of Novel Candidate
Laboratory Investigation (2015) 95, 1077–1088 © 2015 USCAP, Inc All rights reserved 0023-6837/15 Identification, by systematic RNA sequencing, of novel candidate biomarkers and therapeutic targets in human soft tissue tumors Anne E Sarver1, Aaron L Sarver2, Venugopal Thayanithy1 and Subbaya Subramanian1 Human sarcomas comprise a heterogeneous group of more than 50 subtypes broadly classified into two groups: bone and soft tissue sarcomas. Such heterogeneity and their relative rarity have made them challenging targets for classification, biomarker identification, and development of improved treatment strategies. In this study, we used RNA sequencing to analyze 35 primary human tissue samples representing 13 different sarcoma subtypes, along with benign schwannoma, and normal bone and muscle tissues. For each sarcoma subtype, we detected unique messenger RNA (mRNA) expression signatures, which we further subjected to bioinformatic functional analysis, upstream regulatory analysis, and microRNA (miRNA) targeting analysis. We found that, for each sarcoma subtype, significantly upregulated genes and their deduced upstream regulators included not only previously implicated known players but also novel candidates not previously reported to be associated with sarcoma. For example, the schwannoma samples were characterized by high expression of not only the known associated proteins GFAP and GAP43 but also the novel player GJB6. Further, when we integrated our expression profiles with miRNA expression data from each sarcoma subtype, we were able to deduce potential key miRNA–gene regulator relationships for each. In the Ewing’s sarcoma and fibromatosis samples, two sarcomas where miR-182-5p is significantly downregulated, multiple predicted targets were significantly upregulated, including HMCN1, NKX2-2, SCNN1G, and SOX2. -
Product Name: NDSP/FAM163A Polyclonal Antibody, Cy3 Conjugated Catalog No
Product Name: NDSP/FAM163A Polyclonal Antibody, Cy3 Conjugated Catalog No. : TAP01-88289R-Cy3 Intended Use: For Research Use Only. Not for used in diagnostic procedures. Size 100ul Concentration 1ug/ul Gene ID ISO Type Rabbit IgG Clone N/A Immunogen Range Conjugation Cy3 Subcellular Locations Applications IF(IHC-P) Cross Reactive Species Human, Mouse, Rat Source KLH conjugated synthetic peptide derived from human NDSP Applications with IF(IHC-P)(1:50-200) Dilutions Purification Purified by Protein A. Background Chromosome 1 is the largest human chromosome spanning about 260 million base pairs and making up 8% of the human genome. There are about 3,000 genes on chromosome 1, and considering the great number of genes there are also a large number of diseases associated with chromosome 1. Notably, the rare aging disease Hutchinson-Gilford progeria is associated with the LMNA gene which encodes lamin A. When defective, the LMNA gene product can build up in the nucleus and cause characteristic nuclear blebs. The mechanism of rapidly enhanced aging is unclear and is a topic of continuing exploration. The MUTYH gene is located on chromosome 1 and is partially responsible for familial adenomatous polyposis. Stickler syndrome, Parkinsons, Gaucher disease and Usher syndrome are also associated with chromosome 1. A breakpoint has been identified in 1q which disrupts the DISC1 gene and is linked to schizophrenia. Aberrations in chromosome 1 are found in a variety of cancers including head and neck cancer, malignant melanomaand multiple myeloma. The C1orf76 gene product has been provisionally designated C1orf76 pending further characterization. Synonyms C1orf76; Chromosome 1 open reading frame 76; F163A_HUMAN; Fam163a; hypothetical protein MGC16664; NDSP; Neuroblastoma derived secretory protein; Neuroblastoma-derived secretory protein; Protein FAM163A Storage Aqueous buffered solution containing 1% BSA, 50% glycerol and 0.09% sodium azide. -
Mouse Fam163a Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Fam163a Knockout Project (CRISPR/Cas9) Objective: To create a Fam163a knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Fam163a gene (NCBI Reference Sequence: NM_177838 ; Ensembl: ENSMUSG00000015484 ) is located on Mouse chromosome 1. 5 exons are identified, with the ATG start codon in exon 4 and the TAA stop codon in exon 5 (Transcript: ENSMUST00000015628). Exon 4~5 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 4 starts from about 0.2% of the coding region. Exon 4~5 covers 100.0% of the coding region. The size of effective KO region: ~1143 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 4 5 Legends Exon of mouse Fam163a Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of start codon is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of stop codon is aligned with itself to determine if there are tandem repeats. -
Quantitative Trait Loci Mapping of Macrophage Atherogenic Phenotypes
QUANTITATIVE TRAIT LOCI MAPPING OF MACROPHAGE ATHEROGENIC PHENOTYPES BRIAN RITCHEY Bachelor of Science Biochemistry John Carroll University May 2009 submitted in partial fulfillment of requirements for the degree DOCTOR OF PHILOSOPHY IN CLINICAL AND BIOANALYTICAL CHEMISTRY at the CLEVELAND STATE UNIVERSITY December 2017 We hereby approve this thesis/dissertation for Brian Ritchey Candidate for the Doctor of Philosophy in Clinical-Bioanalytical Chemistry degree for the Department of Chemistry and the CLEVELAND STATE UNIVERSITY College of Graduate Studies by ______________________________ Date: _________ Dissertation Chairperson, Johnathan D. Smith, PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, David J. Anderson, PhD Department of Chemistry, Cleveland State University ______________________________ Date: _________ Dissertation Committee member, Baochuan Guo, PhD Department of Chemistry, Cleveland State University ______________________________ Date: _________ Dissertation Committee member, Stanley L. Hazen, MD PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, Renliang Zhang, MD PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, Aimin Zhou, PhD Department of Chemistry, Cleveland State University Date of Defense: October 23, 2017 DEDICATION I dedicate this work to my entire family. In particular, my brother Greg Ritchey, and most especially my father Dr. Michael Ritchey, without whose support none of this work would be possible. I am forever grateful to you for your devotion to me and our family. You are an eternal inspiration that will fuel me for the remainder of my life. I am extraordinarily lucky to have grown up in the family I did, which I will never forget.