Database Mining with Biomart
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RNA Sequencing Reveals a Slow to Fast Muscle Fiber Type Transition After Olanzapine Infusion in Rats
RESEARCH ARTICLE RNA Sequencing Reveals a Slow to Fast Muscle Fiber Type Transition after Olanzapine Infusion in Rats Christopher J. Lynch1*, Yuping Xu1, Andras Hajnal2, Anna C. Salzberg3, Yuka Imamura Kawasawa4,5,6 1 Department of Cellular and Molecular Physiology, College of Medicine, Penn State University, Hershey, Pennsylvania, 17033, United States of America, 2 Department of Neural and Behavioral Sciences, College of Medicine, Penn State University, Hershey, Pennsylvania, 17033, United States of America, 3 Department a11111 of Public Health Sciences, College of Medicine, Penn State University, Hershey, Pennsylvania, 17033, United States of America, 4 Department of Pharmacology, College of Medicine, Penn State University, Hershey, Pennsylvania, 17033, United States of America, 5 Department of Biochemistry and Molecular Biology, College of Medicine, Penn State University, Hershey, Pennsylvania, 17033, United States of America, 6 The Institute for Personalized Medicine, College of Medicine, Penn State University, Hershey, Pennsylvania, 17033, United States of America * [email protected] OPEN ACCESS Citation: Lynch CJ, Xu Y, Hajnal A, Salzberg AC, Kawasawa YI (2015) RNA Sequencing Reveals a Abstract Slow to Fast Muscle Fiber Type Transition after Olanzapine Infusion in Rats. PLoS ONE 10(4): Second generation antipsychotics (SGAs), like olanzapine, exhibit acute metabolic side ef- e0123966. doi:10.1371/journal.pone.0123966 fects leading to metabolic inflexibility, hyperglycemia, adiposity and diabetes. Understand- Academic Editor: Guillermo López Lluch, ing how SGAs affect the skeletal muscle transcriptome could elucidate approaches for Universidad Pablo de Olavide, Centro Andaluz de mitigating these side effects. Male Sprague-Dawley rats were infused intravenously with ve- Biología del Desarrollo-CSIC, SPAIN hicle or olanzapine for 24h using a dose leading to a mild hyperglycemia. -
Description of the Biomart Package
Description of the biomaRt package Steffen Durinck‡∗, Wolfgang Huber¶†, Yves Moreau‡, Bart De Moor‡ July 25, 2006 ‡Department of Electronical Engineering, ESAT-SCD, K.U.Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium, http://www.esat.kuleuven.ac.be/~dna/BioI and ¶European Bioinformatics Institute, Hinxton, UK Contents 1 Introduction 2 2 objects 2 2.1 Mart-class..................................... 2 3 Simple biomaRt functions for frequently used queries to Ensembl 3 3.1 Selecting a BioMart database to use . 3 3.1.1 useMart .................................. 3 3.1.2 martDisconnect ............................. 3 3.2 Annotating identifiers with gene information . 4 3.2.1 GOannotation .............................. 6 3.2.2 OMIMannotation ............................ 7 3.2.3 INTERPRO protein domains . 7 3.3 Homologymapping................................ 8 3.4 Identify subsets of genes for further analysis with the getFeature function . 8 3.5 Sequenceinformation............................... 9 3.6 Single Nucleotide Polymorphisms . 9 3.7 Moreexoticfunctions............................... 10 3.7.1 getPossibleXrefs ............................ 10 3.7.2 getXref .................................. 10 ∗Steff[email protected] †[email protected] 1 4 Advanced data retrieval with BioMart API functions 10 4.1 listMarts...................................... 11 4.2 useMart ...................................... 11 4.3 listDatasets .................................... 11 4.4 useDataset..................................... 12 4.5 Filter, Values and Attributes . 12 5 Local BioMart databases 13 1 Introduction The BioConductor biomaRt package provides and API in R to query BioMart databases such as Ensembl (http://www.ensembl.org), a software system which produces and maintains au- tomatic annotation on metazoan genomes. Two sets of functions are currently implemented. A first set of functions is tailored towards Ensembl and are a set of commonly used queries in microarray data analysis. -
Spontaneous Puberty in 46,XX Subjects with Congenital Lipoid Adrenal Hyperplasia
Spontaneous puberty in 46,XX subjects with congenital lipoid adrenal hyperplasia. Ovarian steroidogenesis is spared to some extent despite inactivating mutations in the steroidogenic acute regulatory protein (StAR) gene. K Fujieda, … , T Sugawara, J F Strauss 3rd J Clin Invest. 1997;99(6):1265-1271. https://doi.org/10.1172/JCI119284. Research Article Congenital lipoid adrenal hyperplasia (lipoid CAH) is the most severe form of CAH in which the synthesis of all gonadal and adrenal cortical steroids is markedly impaired. We report here the clinical, endocrinological, and molecular analyses of two unrelated Japanese kindreds of 46,XX subjects affected with lipoid CAH who manifested spontaneous puberty. Phenotypic female infants with 46,XX karyotypes were diagnosed with lipoid CAH as newborns based on a clinical history of failure to thrive, hyperpigmentation, hyponatremia, hyperkalemia, and low basal values of serum cortisol and urinary 17-hydroxycorticosteroid and 17-ketosteroid. These patients responded to treatment with glucocorticoid and 9alpha- fludrocortisone. Spontaneous thelarche occurred in association with increased serum estradiol levels at the age of 10 and 11 yr, respectively. Pubic hair developed at the age of 12 yr 11 mo in one subject and menarche was at the age of 12 yr in both cases. Both subjects reported periodic menstrual bleeding and subsequently developed polycystic ovaries. To investigate the molecular basis of the steroidogenic lesion in these patients, the StAR gene was characterized by PCR and direct DNA sequence -
Early Diagnosis of Colorectal Cancer Via Plasma Proteomic Analysis of CRC and Advanced Adenomatous Polyp
Gastroenterology and Hepatology From Bed to Bench. ORIGINAL ARTICLE ©2019 RIGLD, Research Institute for Gastroenterology and Liver Diseases Early diagnosis of colorectal cancer via plasma proteomic analysis of CRC and advanced adenomatous polyp Setareh Fayazfar1, Hakimeh Zali2, Afsaneh Arefi Oskouie1, Hamid Asadzadeh Aghdaei3, Mostafa Rezaei Tavirani4, Ehsan Nazemalhosseini Mojarad5 1Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran 2School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran 3Basic and Molecular Epidemiology of Gastroenterology Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran 4Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran 5Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran ABSTRACT Aim: This paper aimed to identify new candidate biomarkers in blood for early diagnosis of CRC. Background: Colorectal cancer (CRC) is the third most widespread malignancies increasing globally. The high mortality rate associated with colorectal cancer is due to the delayed diagnosis in an advanced stage while the metastasis has occurred. For better clinical management and subsequently to reduce mortality of CRC, early detection biomarkers are in high demand. -
Nonclassic Congenital Lipoid Adrenal Hyperplasia Diagnosed at 17 Months in a Korean Boy with Normal Male Genitalia: Emphasis on Pigmentation As a Diagnostic Clue
Case report https://doi.org/10.6065/apem.2020.25.1.46 Ann Pediatr Endocrinol Metab 2020;25:4651 Nonclassic congenital lipoid adrenal hyperplasia diagnosed at 17 months in a Korean boy with normal male genitalia: emphasis on pigmentation as a diagnostic clue Hosun Bae, MD1, Congenital lipoid adrenal hyperplasia (CLAH) is one of the most fatal conditions Min-Sun Kim, MD1, caused by an abnormality of adrenal and gonadal steroidogenesis. CLAH results Hyojung Park, MD1, from loss-of-function mutations of the steroidogenic acute regulatory (STAR) Ja-Hyun Jang, MD, PhD2, gene; the disease manifests with electrolyte imbalances and hyperpigmentation Jong-Moon Choi, MD, PhD2, in neonates or young infants due to adrenocortical hormone deficiencies, and 46, Sae-Mi Lee, MD, PhD2, XY genetic male CLAH patients can be phenotypically female. Meanwhile, some Sung Yoon Cho, MD, PhD1, patients with STAR mutations develop hyperpigmentation and mild signs of adrenal insufficiency, such as hypoglycemia, after infancy. These patients are classified as Dong-Kyu Jin, MD, PhD1 having nonclassic CLAH (NCCLAH) caused by STAR mutations that retain partial 1Department of Pediatrics, Samsung activity of STAR. We present the case of a Korean boy with normal genitalia who Medical Center, Sungkyunkwan Univer was diagnosed with NCCLAH. He presented with whole-body hyperpigmentation sity School of Medicine, Seoul, Korea and electrolyte abnormalities, which were noted at the age of 17 months after 2GC Genome, Yongin, Korea an episode of sepsis with peritonitis. The compound heterozygous mutations p.Gly221Ser and c.653C>T in STAR were identified by targeted gene-panel sequencing. Skin hyperpigmentation should be considered an important clue for diagnosing NCCLAH. -
Epigenomics Profiling Services
EPIGENOMICS PROFILING SERVICES • Chromatin analysis • DNA methylation analysis • RNA-seq analysis Diagenode helps you uncover the mysteries of epigenetics PAGE 3 Integrative epigenomics analysis DNA methylation analysis • Reduced representation bisulfite sequencing (RRBS) • Whole genome bisulfite sequencing analysis (WGBS) • Genome-wide DNA methylation • Differentially methylated region analysis DNA Chromatin RNA ChIP-seq/ChIP-qPCR analysis RNA-seq analysis • Histone modification ChIP-seq analysis • Small RNA-sequencing • Promoter analysis • mRNA analysis • Enhancer analysis • Whole transcriptome analysis • Transcription factor ChIP-seq analysis • Gene expression profiling • Customized NGS service • Chromatin accessibility (ATAC-seq) www.diagenode.com | PAGE 4 DIAGENODE EPIGENOMICS PROFILING SERVICES Expertise that you can trust Our Epigenomics Profiling Services assure the sample preparation expertise and quality data that you seek. We provide epigenome-wide analyses for understanding epigenetic mechanisms, epigenetics-related drug discovery, epigenetic biomarker identification, and functional epigenomics. Why Diagenode? • Expertise and trust: Recognized epigenetics leader, official partner of BLUEPRINT, IHEC and FAANG • Innovative technology: Utilization of the signature Bioruptor® sonication device for optimal chromatin and DNA shearing and the IP-Star® Automation device give reproducible and reliable optimization and results • Quality: Multiple QC steps in all workflows and validated antibodies plus reagents deliver superior data Human -
High-Throughput Bioinformatics Approaches to Understand Gene Expression Regulation in Head and Neck Tumors
High-throughput bioinformatics approaches to understand gene expression regulation in head and neck tumors by Yanxiao Zhang A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Bioinformatics) in The University of Michigan 2016 Doctoral Committee: Associate Professor Maureen A. Sartor, Chair Professor Thomas E. Carey Assistant Professor Hui Jiang Professor Ronald J. Koenig Associate Professor Laura M. Rozek Professor Kerby A. Shedden c Yanxiao Zhang 2016 All Rights Reserved I dedicate this thesis to my family. For their unfailing love, understanding and support. ii ACKNOWLEDGEMENTS I would like to express my gratitude to Dr. Maureen Sartor for her guidance in my research and career development. She is a great mentor. She patiently taught me when I started new in this field, granted me freedom to explore and helped me out when I got lost. Her dedication to work, enthusiasm in teaching, mentoring and communicating science have inspired me to feel the excite- ment of research beyond novel scientific discoveries. I’m also grateful to have an interdisciplinary committee. Their feedback on my research progress and presentation skills is very valuable. In particular, I would like to thank Dr. Thomas Carey and Dr. Laura Rozek for insightful discussions on the biology of head and neck cancers and human papillomavirus, Dr. Ronald Koenig for expert knowledge on thyroid cancers, Dr. Hui Jiang and Dr. Kerby Shedden for feedback on the statistics part of my thesis. I would like to thank all the past and current members of Sartor lab for making the lab such a lovely place to stay and work in. -
Long-Term Follow-Up in a Chinese Child with Congenital Lipoid Adrenal
Zhao et al. BMC Endocrine Disorders (2018) 18:78 https://doi.org/10.1186/s12902-018-0307-6 CASEREPORT Open Access Long-term follow-up in a Chinese child with congenital lipoid adrenal hyperplasia due to a StAR gene mutation Xiu Zhao1,ZheSu1* , Xia Liu1,JianmingSong2,YungenGan3, Pengqiang Wen4,ShoulinLi5,LiWang1 and Lili Pan1 Abstract Background: Congenital lipoid adrenal hyperplasia (CLAH) is an extremely rare and the most severe form of congenital adrenal hyperplasia. Typical features include disorder of sex development, early-onset adrenal crisis and enlarged adrenal glands with fatty accumulation. Case presentation: We report a case of CLAH caused by mutations in the steroidogenic acute regulatory protein (StAR) gene. The patient had typical early-onset adrenal crisis at 2 months of age. She had normal-appearing female genitalia and a karyotype of 46, XY. The serum cortisol and adrenal steroids levels were always nearly undetectable, but the adrenocorticotropic hormone levels were extremely high. Genetic analysis revealed compound heterozygous mutations at c. 229C > T (p.Q77X) in exon 3 and c. 722C > T (p.Q258X) in exon 7 of the StAR gene. The former mutation was previously detected in only two other Chinese CLAH patients. Both mutations cause truncation of the StAR protein.Thecasereportedhereappearstobeaclassicexample of CLAH with very small adrenal glands and is the second reported CLAH case with small adrenal glands thus far. In a 15-year follow-up, the patient’sheight wasapproximatelyaverageforfemalesbeforeage4andfellto− 1 SDS at 10 years of age. Her bone age was similar to her chronological age from age 4 to age 15 years. Conclusions: In conclusion, this is a classic case of CLAH with exceptionally small adrenal glands. -
"The Genecards Suite: from Gene Data Mining to Disease Genome Sequence Analyses". In: Current Protocols in Bioinformat
The GeneCards Suite: From Gene Data UNIT 1.30 Mining to Disease Genome Sequence Analyses Gil Stelzer,1,5 Naomi Rosen,1,5 Inbar Plaschkes,1,2 Shahar Zimmerman,1 Michal Twik,1 Simon Fishilevich,1 Tsippi Iny Stein,1 Ron Nudel,1 Iris Lieder,2 Yaron Mazor,2 Sergey Kaplan,2 Dvir Dahary,2,4 David Warshawsky,3 Yaron Guan-Golan,3 Asher Kohn,3 Noa Rappaport,1 Marilyn Safran,1 and Doron Lancet1,6 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 2LifeMap Sciences Ltd., Tel Aviv, Israel 3LifeMap Sciences Inc., Marshfield, Massachusetts 4Toldot Genetics Ltd., Hod Hasharon, Israel 5These authors contributed equally to the paper 6Corresponding author GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It au- tomatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. Var- Elect’s capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. -
Gene Mapping and Medical Genetics
J Med Genet: first published as 10.1136/jmg.24.8.451 on 1 August 1987. Downloaded from Gene mapping and medical genetics Journal of Medical Genetics 1987, 24, 451-456 Molecular genetics of human chromosome 16 GRANT R SUTHERLAND*, STEPHEN REEDERSt, VALENTINE J HYLAND*, DAVID F CALLEN*, ANTONIO FRATINI*, AND JOHN C MULLEY* From *the Cytogenetics Unit, Adelaide Children's Hospital, North Adelaide, South Australia 5006; and tUniversity of Oxford, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DU. SUMMARY The major diseases mapped to chromosome 16 are adult polycystic kidney disease and those resulting from mutations in the a globin complex. There are at least six other less important genetic diseases which map to this chromosome. The adenine phosphoribosyltransferase gene allows for selection of chromosome 16 in somatic cell hybrids and a hybrid panel is available which segments the chromosome into six regions to facilitate gene mapping. Genes which have been mapped to this chromosome or which have had their location redefined since HGM8 include APRT, TAT, MT, HBA, PKDI, CTRB, PGP, HAGH, HP, PKCB, and at least 19 cloned DNA sequences. There are RFLPs at 13 loci which have been regionally mapped and can be used for linkage studies. Chromosome 16 is not one of the more extensively have been cloned and mapped to this chromosome. mapped human autosomes. However, it has a Brief mention will be made of a hybrid cell panel http://jmg.bmj.com/ number of features which make it attractive to the which allows for an efficient regional localisation of gene mapper. -
The Biomart User's Guide
The biomaRt user's guide Steffen Durinck,∗ Wolfgang Hubery September 15, 2015 Contents 1 Introduction 2 2 Selecting a BioMart database and dataset 3 3 How to build a biomaRt query 7 4 Examples of biomaRt queries 9 4.1 Task 1: Annotate a set of Affymetrix identifiers with HUGO symbol and chromosomal locations of corresponding genes . 9 4.2 Task 2: Annotate a set of EntrezGene identifiers with GO annotation . 9 4.3 Task 3: Retrieve all HUGO gene symbols of genes that are located on chromosomes 17,20 or Y , and are associated with one the following GO terms: "GO:0051330","GO:0000080","GO:0000114","GO:0000082" (here we'll use more than one filter) . 10 4.4 Task 4: Annotate set of idenfiers with INTERPRO protein domain identifiers . 10 4.5 Task 5: Select all Affymetrix identifiers on the hgu133plus2 chip and Ensembl gene identifiers for genes located on chro- mosome 16 between basepair 1100000 and 1250000. 11 4.6 Task 6: Retrieve all entrezgene identifiers and HUGO gene symbols of genes which have a "MAP kinase activity" GO term associated with it. 11 ∗[email protected] [email protected] 1 4.7 Task 7: Given a set of EntrezGene identifiers, retrieve 100bp upstream promoter sequences . 12 4.8 Task 8: Retrieve all 5' UTR sequences of all genes that are located on chromosome 3 between the positions 185514033 and 185535839 . 13 4.9 Task 9: Retrieve protein sequences for a given list of Entrez- Gene identifiers . 13 4.10 Task 10: Retrieve known SNPs located on the human chro- mosome 8 between positions 148350 and 148612 . -
The T(6;16)(P21;Q22) Chromosome Translocation in the Lncap Prostate Carcinoma Cell Line Results in a Tpc/Hpr Fusion Gene'
CANCERRESEARCH56.728-732.February15. 9961 Advances in Brief The t(6;16)(p21;q22) Chromosome Translocation in the LNCaP Prostate Carcinoma Cell Line Results in a tpc/hpr Fusion Gene' Maria Luisa Veronese, Florencia Bulinch, Massimo Negrini, and Carlo M. Croce2 Jefferson Cancer Center, Jefferson Cancer Institute and Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107 Abstract level. We have found that the translocation results in fusion of the hpr gene on chromosome 16 to the tpc gene, a novel gene coding for a Very little is known about the molecular and genetic mechanisms protein similar to nbosomal protein 510. involved in prostate cancer.Previousstudieshaveshownfrequent lossof heterozygosity(40%)at chromosomalregions8p, lOq,and 16q,suggesting thepresenceoftumorsuppressorgenesintheseregions.TheLNCaP cell Materials and Methods line, establishedfrom a metastaticlesionof human prostatic adenocarci Rodent-Human Hybrids. The hybrids seriesA9LN were obtainedfrom noma,carries a t(6;16)(p21;q22)translocation.To determinewhether this translocation involved genesimportant in the processof malignant trans thefusionof thehumanprostatecarcinomacellline LNCaPandthemouseA9 formation, weclonedand sequencedthet(6;16) breakpoint ofthis cell line. cell line as previously described (15). PCR analysis with primers from both the Sequenceanalysisshowedthat the breakpoint is within the haptoglobin shortandlongarmsof chromosome16wascarriedout in 1 X PCRbufferwith geneclusteron chromosome16,and that, on chromosome6,the break MgCI2 (Boehringer Mannheim) with 100 ng template DNA, 100 ng each of occurs within a novel gene,tpc, similar to the prokaryotic SlO ribosomal forward and reverseprimer, 250 @Mdeoxynucleotidetriphosphates(Perkin protein gene. The translocation results in the production of a fusion Elmer/Cetus), and 0.5 units of Taq DNA polymerase (Boehringer Mannheim) transcript, tpc/hpr.