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Old Data and Friends Improve with Age: Advancements with the Updated Tools of Genenetwork
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.24.445383; this version posted May 25, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. Old data and friends improve with age: Advancements with the updated tools of GeneNetwork Alisha Chunduri1, David G. Ashbrook2 1Department of Biotechnology, Chaitanya Bharathi Institute of Technology, Hyderabad 500075, India 2Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA Abstract Understanding gene-by-environment interactions is important across biology, particularly behaviour. Families of isogenic strains are excellently placed, as the same genome can be tested in multiple environments. The BXD’s recent expansion to 140 strains makes them the largest family of murine isogenic genomes, and therefore give great power to detect QTL. Indefinite reproducible genometypes can be leveraged; old data can be reanalysed with emerging tools to produce novel biological insights. To highlight the importance of reanalyses, we obtained drug- and behavioural-phenotypes from Philip et al. 2010, and reanalysed their data with new genotypes from sequencing, and new models (GEMMA and R/qtl2). We discover QTL on chromosomes 3, 5, 9, 11, and 14, not found in the original study. We narrowed down the candidate genes based on their ability to alter gene expression and/or protein function, using cis-eQTL analysis, and variants predicted to be deleterious. Co-expression analysis (‘gene friends’) and human PheWAS were used to further narrow candidates. -
Sex-Specific Hippocampal 5-Hydroxymethylcytosine Is Disrupted in Response to Acute Stress Ligia A
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications, Department of Statistics Statistics, Department of 2016 Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress Ligia A. Papale University of Wisconsin, [email protected] Sisi Li University of Wisconsin, [email protected] Andy Madrid University of Wisconsin, [email protected] Qi Zhang University of Nebraska-Lincoln, [email protected] Li Chen Emory University See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/statisticsfacpub Part of the Other Statistics and Probability Commons Papale, Ligia A.; Li, Sisi; Madrid, Andy; Zhang, Qi; Chen, Li; Chopra, Pankaj; Jin, Peng; Keles, Sunduz; and Alisch, Reid S., "Sex- specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress" (2016). Faculty Publications, Department of Statistics. 62. https://digitalcommons.unl.edu/statisticsfacpub/62 This Article is brought to you for free and open access by the Statistics, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications, Department of Statistics by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Ligia A. Papale, Sisi Li, Andy Madrid, Qi Zhang, Li Chen, Pankaj Chopra, Peng Jin, Sunduz Keles, and Reid S. Alisch This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/statisticsfacpub/62 Neurobiology of Disease 96 (2016) 54–66 Contents lists available at ScienceDirect Neurobiology of Disease journal homepage: www.elsevier.com/locate/ynbdi Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress Ligia A. Papale a,1,SisiLia,c,1, Andy Madrid a,c,QiZhangd,LiChene,PankajChoprae,PengJine, Sündüz Keleş b, Reid S. -
Single Nucleotide Polymorphisms Within Calcineurin-Encoding Genes
Annals of Applied Sport Science, vol. 4, no. 2, pp. 01-08, Summer 2016 DOI: 10.18869/acadpub.aassjournal.4.2.1 Original Article www.aassjournal.com www.AESAsport.com ISSN (Online): 2322 – 4479 Received: 06/03/2016 ISSN (Print): 2476–4981 Accepted: 26/06/2016 Single Nucleotide Polymorphisms within Calcineurin-Encoding Genes are Associated with Response to Aerobic Training in Han Chinese Males 1Rong-mei Xu, 2Tao Lu, 2Lingxian Yan, 1Qinghua Song* 1The Center of Physical Health, Henan Polytechnic University, Jiaozuo 454000, Henan Province, China. 2 The Lab of Human Body Science, Henan Polytechnic University, Jiaozuo 454000, Henan Province, China. ABSTRACT Calcineurin, which functions in calcium signaling, is expressed in skeletal and cardiac muscle and has been linked to sensitivity to muscle strength training. It is also proposed to contribute to individual aerobic endurance. To investigate the relationship between calcineurin-encoding genes and aerobic endurance traits, 126 young-adult Han Chinese males were enrolled in an aerobic exercise training study. Participants were genotyped for polymorphisms within the 5 genes (PPP3CA, PPP3CB, PPP3CC, PPP3R1 and PPP3R2) encoding calcineurin using restriction fragment length polymorphism polymerase chain reaction (PCR-RFLP) or matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Participants underwent 18 weeks of aerobic exercise training (running). Before and after the training period, maximal oxygen uptake (VO2max) and 12 km/h running economy were measured. Statistical analyses were performed using chi-square test and analysis of variance. The baseline value of VO2max was significantly associated with rs3804423 and rs2850965 loci in the PPP3CA gene (P<0.05). -
List of Genes Associated with Sudden Cardiac Death (Scdgseta) Gene
List of genes associated with sudden cardiac death (SCDgseta) mRNA expression in normal human heart Entrez_I Gene symbol Gene name Uniprot ID Uniprot name fromb D GTEx BioGPS SAGE c d e ATP-binding cassette subfamily B ABCB1 P08183 MDR1_HUMAN 5243 √ √ member 1 ATP-binding cassette subfamily C ABCC9 O60706 ABCC9_HUMAN 10060 √ √ member 9 ACE Angiotensin I–converting enzyme P12821 ACE_HUMAN 1636 √ √ ACE2 Angiotensin I–converting enzyme 2 Q9BYF1 ACE2_HUMAN 59272 √ √ Acetylcholinesterase (Cartwright ACHE P22303 ACES_HUMAN 43 √ √ blood group) ACTC1 Actin, alpha, cardiac muscle 1 P68032 ACTC_HUMAN 70 √ √ ACTN2 Actinin alpha 2 P35609 ACTN2_HUMAN 88 √ √ √ ACTN4 Actinin alpha 4 O43707 ACTN4_HUMAN 81 √ √ √ ADRA2B Adrenoceptor alpha 2B P18089 ADA2B_HUMAN 151 √ √ AGT Angiotensinogen P01019 ANGT_HUMAN 183 √ √ √ AGTR1 Angiotensin II receptor type 1 P30556 AGTR1_HUMAN 185 √ √ AGTR2 Angiotensin II receptor type 2 P50052 AGTR2_HUMAN 186 √ √ AKAP9 A-kinase anchoring protein 9 Q99996 AKAP9_HUMAN 10142 √ √ √ ANK2/ANKB/ANKYRI Ankyrin 2 Q01484 ANK2_HUMAN 287 √ √ √ N B ANKRD1 Ankyrin repeat domain 1 Q15327 ANKR1_HUMAN 27063 √ √ √ ANKRD9 Ankyrin repeat domain 9 Q96BM1 ANKR9_HUMAN 122416 √ √ ARHGAP24 Rho GTPase–activating protein 24 Q8N264 RHG24_HUMAN 83478 √ √ ATPase Na+/K+–transporting ATP1B1 P05026 AT1B1_HUMAN 481 √ √ √ subunit beta 1 ATPase sarcoplasmic/endoplasmic ATP2A2 P16615 AT2A2_HUMAN 488 √ √ √ reticulum Ca2+ transporting 2 AZIN1 Antizyme inhibitor 1 O14977 AZIN1_HUMAN 51582 √ √ √ UDP-GlcNAc: betaGal B3GNT7 beta-1,3-N-acetylglucosaminyltransfe Q8NFL0 -
Leukaemia Section
Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Leukaemia Section Short Communication t(4;9)(q21.22;p24) SEC31A/JAK2 Julie Sanford Biggerstaff Idaho Cytogenetics Diagnostic Laboratory, Boise, ID 83706, USA; [email protected] Published in Atlas Database: April 2017 Online updated version : http://AtlasGeneticsOncology.org/Anomalies/t0409q21p24ID1682.html Printable original version : http://documents.irevues.inist.fr/bitstream/handle/2042/68905/04-2017-t0409q21p24ID1682.pdf DOI: 10.4267/2042/68905 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2018 Atlas of Genetics and Cytogenetics in Oncology and Haematology Abstract Cytogenetics Review on t(4;9)(q21.22;p24) SEC31A/JAK2, with data on clinics, and the genes involved. Cytogenetics morphological KEYWORDS JAK2 breakapart (commonly available). Chromosome 4; chromosome 9; translocation; SEC31A; JAK2; Hodgkin Lymphoma Genes involved and Clinics and pathology proteins SEC31A (SEC31 homolog A, COPII Disease coat complex component) Hodgkin Lymphoma Location Phenotype/cell stem origin 4q21.22 Hodgkin and Reed-Sternberg cells, which derive DNA/RNA from pre-apoptotic crippled germinal center (GC) B- gene is 72,606 bp with 25 exons; transcribed from cells, are positive for CD30, CD15, CD40 and the - strand; coding region is 62,863 bp with 24 IRF4/MUM1 exons Epidemiology Protein Hodgkin lymphoma itself is common, but this 1166 amnio acids. Protein transport protein SEC31A particular translocation may be rare within the is ubiquitously expressed and forms part of the coat disorder. However, it is not often assayed for; found protein complex II (COPII) which is comprised of at in 2/131 cHL cases examined: a M/31 with nodular least four other proteins in addition to SEC31A this sclerosis cHL, alive 60 mths after diagnosis; and a complex is involved in formation of transport M/83 with lymphocyte-depleted cHL who died at vesicles from the ER to Golgi. -
Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights Into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle
animals Article Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle Masoumeh Naserkheil 1 , Abolfazl Bahrami 1 , Deukhwan Lee 2,* and Hossein Mehrban 3 1 Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; [email protected] (M.N.); [email protected] (A.B.) 2 Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si, Gyeonggi-do 17579, Korea 3 Department of Animal Science, Shahrekord University, Shahrekord 88186-34141, Iran; [email protected] * Correspondence: [email protected]; Tel.: +82-31-670-5091 Received: 25 August 2020; Accepted: 6 October 2020; Published: 9 October 2020 Simple Summary: Hanwoo is an indigenous cattle breed in Korea and popular for meat production owing to its rapid growth and high-quality meat. Its yearling weight and carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score) are economically important for the selection of young and proven bulls. In recent decades, the advent of high throughput genotyping technologies has made it possible to perform genome-wide association studies (GWAS) for the detection of genomic regions associated with traits of economic interest in different species. In this study, we conducted a weighted single-step genome-wide association study which combines all genotypes, phenotypes and pedigree data in one step (ssGBLUP). It allows for the use of all SNPs simultaneously along with all phenotypes from genotyped and ungenotyped animals. Our results revealed 33 relevant genomic regions related to the traits of interest. -
Profilin-1 Is Required for Survival of Adult Hematopoietic Stem Cells
Extended methods Immunohistochemistry HepG-2, SMMC-7721, and 293T cells were obtained from Cell Resource Center of Shanghai Institute for Biological Science, Chinese Academy Science, Shanghai, China. HUVEC cells were kindly provided by Prof. Ping-Jin Gao at Institute of Health Sciences (Shanghai, China). All these cell lines were cultured in DMEM with 10% FBS. MDA- MB-231 cell line was kindly provided by Prof. Ming-Yao Liu (East China Normal University, Shanghai, China) and was cultured in Leibovitz L-15 medium with 10% FBS. All these cell lines were originally purchased from ATCC. MDA-MB-231, SMMC-7721 or HepG2 cells were grown on coverslips in 24-well plates and fixed in either 4% paraformaldehyde or pre-chilled methanol (-20°C) for 10 min. In some cases, WT or VPS33B-null Lin-Sca-1+c-Kit+Flk2-CD34- LT-HSCs were collected by flow cytometry and fixed for immunofluorescence staining. Cells were then blocked with 3% BSA in PBS for 60 min followed by incubation with primary antibodies overnight. The antibodies used were anti-HA (Sigma), anti-Flag (Sigma), anti-VPS33B (Sigma), anti- VPS16B (Abcam), anti-GDI2 (Proteintech), anti-LAMP1 (Proteintech), anti-FLOT1 (Abways), anti-CD63 (Proteintech), anti-ANGPTL2 (R&D system), anti-ANGPTL3 (R&D system), anti-TPO (Abways), anti-GLUT1 (Proteintech), anti-LDHA (Proteintech), anti-PKM2 (CST), anti-RAB11A (Abways), anti-RAB27A (Abways) and anti-V5 (Biodragon). Fluorescent-conjugated secondary antibodies (Alexa Fluor® 488 or Alexa Fluor® 555) against mouse, rabbit, or goat were obtained from the Thermo Scientific Inc. The details for all the antibodies are listed in Table S3. -
Protein Interactions in the Cancer Proteome† Cite This: Mol
Molecular BioSystems View Article Online PAPER View Journal | View Issue Small-molecule binding sites to explore protein– protein interactions in the cancer proteome† Cite this: Mol. BioSyst., 2016, 12,3067 David Xu,ab Shadia I. Jalal,c George W. Sledge Jr.d and Samy O. Meroueh*aef The Cancer Genome Atlas (TCGA) offers an unprecedented opportunity to identify small-molecule binding sites on proteins with overexpressed mRNA levels that correlate with poor survival. Here, we analyze RNA-seq and clinical data for 10 tumor types to identify genes that are both overexpressed and correlate with patient survival. Protein products of these genes were scanned for binding sites that possess shape and physicochemical properties that can accommodate small-molecule probes or therapeutic agents (druggable). These binding sites were classified as enzyme active sites (ENZ), protein–protein interaction sites (PPI), or other sites whose function is unknown (OTH). Interestingly, the overwhelming majority of binding sites were classified as OTH. We find that ENZ, PPI, and OTH binding sites often occurred on the same structure suggesting that many of these OTH cavities can be used for allosteric modulation of Creative Commons Attribution 3.0 Unported Licence. enzyme activity or protein–protein interactions with small molecules. We discovered several ENZ (PYCR1, QPRT,andHSPA6)andPPI(CASC5, ZBTB32,andCSAD) binding sites on proteins that have been seldom explored in cancer. We also found proteins that have been extensively studied in cancer that have not been previously explored with small molecules that harbor ENZ (PKMYT1, STEAP3,andNNMT) and PPI (HNF4A, MEF2B,andCBX2) binding sites. All binding sites were classified by the signaling pathways to Received 29th March 2016, which the protein that harbors them belongs using KEGG. -
Differential Requirements for Tousled-Like Kinases 1 and 2 in Mammalian Development
Cell Death and Differentiation (2017) 24, 1872–1885 & 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved 1350-9047/17 www.nature.com/cdd Differential requirements for Tousled-like kinases 1 and 2 in mammalian development Sandra Segura-Bayona1,8, Philip A Knobel1,8, Helena González-Burón1,8, Sameh A Youssef2,3, Aida Peña-Blanco1, Étienne Coyaud4,5, Teresa López-Rovira1, Katrin Rein1, Lluís Palenzuela1, Julien Colombelli1, Stephen Forrow1, Brian Raught4,5, Anja Groth6, Alain de Bruin2,7 and Travis H Stracker*,1 The regulation of chromatin structure is critical for a wide range of essential cellular processes. The Tousled-like kinases, TLK1 and TLK2, regulate ASF1, a histone H3/H4 chaperone, and likely other substrates, and their activity has been implicated in transcription, DNA replication, DNA repair, RNA interference, cell cycle progression, viral latency, chromosome segregation and mitosis. However, little is known about the functions of TLK activity in vivo or the relative functions of the highly similar TLK1 and TLK2 in any cell type. To begin to address this, we have generated Tlk1- and Tlk2-deficient mice. We found that while TLK1 was dispensable for murine viability, TLK2 loss led to late embryonic lethality because of placental failure. TLK2 was required for normal trophoblast differentiation and the phosphorylation of ASF1 was reduced in placentas lacking TLK2. Conditional bypass of the placental phenotype allowed the generation of apparently healthy Tlk2-deficient mice, while only the depletion of both TLK1 and TLK2 led to extensive genomic instability, indicating that both activities contribute to genome maintenance. Our data identifies a specific role for TLK2 in placental function during mammalian development and suggests that TLK1 and TLK2 have largely redundant roles in genome maintenance. -
Calcineurin a (PPP3CA) (NM 000944) Human Tagged ORF Clone 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 RC219136 Calcineurin A (PPP3CA) (NM_000944) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: Calcineurin A (PPP3CA) (NM_000944) Human Tagged ORF Clone Tag: Myc-DDK Symbol: PPP3CA Synonyms: ACCIID; CALN; CALNA; CALNA1; CCN1; CNA1; IECEE; IECEE1; PPP2B Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin 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 / 5 Calcineurin A (PPP3CA) (NM_000944) Human Tagged ORF Clone – RC219136 ORF Nucleotide >RC219136 representing NM_000944 Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGTCCGAGCCCAAGGCAATTGATCCCAAGTTGTCGACGACCGACAGGGTGGTGAAAGCTGTTCCATTTC CTCCAAGTCACCGGCTTACAGCAAAAGAAGTGTTTGATAATGATGGAAAACCTCGTGTGGATATCTTAAA GGCGCATCTTATGAAGGAGGGAAGGCTGGAAGAGAGTGTTGCATTGAGAATAATAACAGAGGGTGCATCA ATTCTTCGACAGGAAAAAAATTTGCTGGATATTGATGCGCCAGTCACTGTTTGTGGGGACATTCATGGAC AATTCTTTGATTTGATGAAGCTCTTTGAAGTCGGGGGATCTCCTGCCAACACTCGCTACCTCTTCTTAGG GGACTATGTTGACAGAGGGTACTTCAGTATTGAATGTGTGCTGTATTTGTGGGCCTTGAAAATTCTCTAC CCCAAAACACTGTTTTTACTTCGTGGAAATCATGAATGTAGACATCTAACAGAGTATTTCACATTTAAAC AAGAATGTAAAATAAAGTATTCAGAACGCGTATATGATGCCTGTATGGATGCCTTTGACTGCCTTCCCCT -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
The Limb-Girdle Muscular Dystrophies and the Dystrophinopathies Review Article
Review Article 04/25/2018 on mAXWo3ZnzwrcFjDdvMDuzVysskaX4mZb8eYMgWVSPGPJOZ9l+mqFwgfuplwVY+jMyQlPQmIFeWtrhxj7jpeO+505hdQh14PDzV4LwkY42MCrzQCKIlw0d1O4YvrWMUvvHuYO4RRbviuuWR5DqyTbTk/icsrdbT0HfRYk7+ZAGvALtKGnuDXDohHaxFFu/7KNo26hIfzU/+BCy16w7w1bDw== by https://journals.lww.com/continuum from Downloaded Downloaded from Address correspondence to https://journals.lww.com/continuum Dr Stanley Jones P. Iyadurai, Ohio State University, Wexner The Limb-Girdle Medical Center, Department of Neurology, 395 W 12th Ave, Columbus, OH 43210, Muscular Dystrophies and [email protected]. Relationship Disclosure: by mAXWo3ZnzwrcFjDdvMDuzVysskaX4mZb8eYMgWVSPGPJOZ9l+mqFwgfuplwVY+jMyQlPQmIFeWtrhxj7jpeO+505hdQh14PDzV4LwkY42MCrzQCKIlw0d1O4YvrWMUvvHuYO4RRbviuuWR5DqyTbTk/icsrdbT0HfRYk7+ZAGvALtKGnuDXDohHaxFFu/7KNo26hIfzU/+BCy16w7w1bDw== Dr Iyadurai has received the Dystrophinopathies personal compensation for serving on the advisory boards of Allergan; Alnylam Stanley Jones P. Iyadurai, MSc, PhD, MD; John T. Kissel, MD, FAAN Pharmaceuticals, Inc; CSL Behring; and Pfizer, Inc. Dr Kissel has received personal ABSTRACT compensation for serving on a consulting board of AveXis, Purpose of Review: The classic approach to identifying and accurately diagnosing limb- Inc; as journal editor of Muscle girdle muscular dystrophies (LGMDs) relied heavily on phenotypic characterization and & Nerve; and as a consultant ancillary studies including muscle biopsy. Because of rapid advances in genetic sequencing for Novartis AG. Dr Kissel has received research/grant methodologies,