Probabilistic Models for Collecting, Analyzing, and Modeling Expression Data
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Genetic Mutation Analysis of High and Low Igy Chickens by Capture Sequencing
animals Article Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing 1,2, 1,2, 1,3 1,2 1,2 1,2 Qiao Wang y , Fei Wang y, Lu Liu , Qinghe Li , Ranran Liu , Maiqing Zheng , Huanxian Cui 1,2, Jie Wen 1,2 and Guiping Zhao 1,2,4,* 1 Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; [email protected] (Q.W.); [email protected] (F.W.); [email protected] (L.L.); [email protected] (Q.L.); [email protected] (R.L.); [email protected] (M.Z.); [email protected] (H.C.); [email protected] (J.W.) 2 State Key Laboratory of Animal Nutrition, Beijing 100193, China 3 College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China 4 School of Life Science and Engineering, Foshan University, Foshan 528225, China * Correspondence: [email protected] These authors contributed equally to this work. y Received: 6 March 2019; Accepted: 20 May 2019; Published: 23 May 2019 Simple Summary: Immunoglobulin Y (IgY) is the major antibody produced by hens and it endows their offspring with effective humoral immunity against the pathogens. In previous research, we identified 13 genomic regions that were significantly associated with the serum IgY level or antibody responses to sheep red-blood-cells, but the specific mutations in these regions have not been reported. Therefore, we screened for variations in these regions in White Leghorn and Beijing-You chickens with high and low IgY. Our study identified 35,154 mutations and 829 Indels which were associated with IgY levels in both lines. -
E2F1 Interactive with BRCA1 Pathway Induces HCC Two Different Small Molecule Metabolism Or Cell Cycle Regulation Via Mitochondrion Or CD4+T to Cytosol
Received: 29 March 2017 | Accepted: 3 May 2017 DOI: 10.1002/jcp.25988 ORIGINAL RESEARCH ARTICLE E2F1 interactive with BRCA1 pathway induces HCC two different small molecule metabolism or cell cycle regulation via mitochondrion or CD4+T to cytosol Qingchun Chen1 | Lin Wang1 | Minghu Jiang2 | Juxiang Huang1 | Zhenfu Jiang1 | Haitao Feng3 | Zhili Ji4 1 Computation and Systems Biology, School of Electronic Engineering, Beijing University of Breast cancer 1 (BRCA1) and E2F transcription factor 1 (E2F1) are related to metabolism Posts and Telecommunications, Beijing, China and cell cycle regulation. However, the corresponding mechanism is not clear in HCC. 2 Lab of Computational Linguistics, School of Humanities and Social Sciences, Tsinghua High BRCA1 direct pathway was constructed with 11 molecules from E2F1 feedback- University, Beijing, China interactive network in HCC by GRNInfer based on 39 Pearson mutual positive 3 Dean department, Heilongjiang University of corelation CC ≥0.25 molecules with E2F1. Integration of GRNInfer with GO, KEGG, Chinese Medicine, Harbin, China BioCarta, GNF_U133A, UNIGENE_EST, Disease, GenMAPP databases by DAVID and 4 Department of General Surgery, Beijing Luhe Hospital, Capital Medical University, Beijing, China MAS 3.0, E2F1 feedback-interactive BRCA1 indirect mitochondrion to cytosol pathway was identified as upstream LAPTM4B activation, feedback UNG, downstream BCAT1- Correspondence Prof., Dr. Lin Wang, Computation and HIST1H2AD-TK1 reflecting protein, and DNA binding with enrichment of small molecule Systems Biology, School of Electronics metabolism; The corresponding BRCA1 indirect membrane to cytosol pathway as Engineering, Beijing University of Posts and Telecommunications, Beijing, 100876, China. upstream CCNB2-NUSAP1 activation, feedback TTK-HIST1H2BJ-CENPF, downstream (Minghu Jiang c/o Lin Wang). -
Microarray Analysis of Gene Expression in the Ovarian Cancer Cell Line HO-8910 with Silencing of the ZNF217 Gene
MOLECULAR MEDICINE REPORTS 2: 851-855, 2009 851 Microarray analysis of gene expression in the ovarian cancer cell line HO-8910 with silencing of the ZNF217 gene GUIQIN SUN1, JINGXIA QIN1, YUWEN QIU1, YUNFEI GAO1, YANHONG YU1, QINKAI DENG2 and MEI ZHONG1 1Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University; 2Department of Bioinformatics, Southern Medical University, Guangzhou 510515, Guangdong, P.R. China Received April 30, 2009; Accepted July 7, 2009 DOI: 10.3892/mmr_00000183 Abstract. Zinc-finger protein 217 (ZNF217), which is over- late stages (stage III or IV) and have a 5-year survival rate of expressed during cancer progression, can promote tumor cell less than 30% (1). Ovarian cancer is a heterogeneous disease immortalization. To examine the function of ZNF217, a global with respect to its histopathology, molecular biology and expression profile was carried out using Affymetrix Gene clinical outcome. Though studies on the etiology of ovarian Chip analysis with HG-U133 plus 2.0 arrays in the ovarian cancer and susceptibility to the disease have shown that the cancer cell line HO-8910 after silencing of the ZNF217 gene. mechanisms of carcinogenesis and cancer development are The results were analyzed using the Gene Ontology program associated with genetic, epigenetic and environmental factors, to investigate the functional network affected by ZNF217 the pathogenesis of ovarian cancer remains unclear (2). in ovarian cancer cells. Changes in the mRNA expression Among the current methods for the identification of gene of the affected genes were confirmed by real-time reverse expression profiles in cancer, microarray analysis is the most transcriptase-polymerase chain reaction (RT-PCR). -
The Popeye Domain Containing Protein Family E a Novel Class of Camp Effectors with Important Functions in Multiple Tissues
Progress in Biophysics and Molecular Biology xxx (2016) 1e9 Contents lists available at ScienceDirect Progress in Biophysics and Molecular Biology journal homepage: www.elsevier.com/locate/pbiomolbio The Popeye domain containing protein family e A novel class of cAMP effectors with important functions in multiple tissues * Roland F.R. Schindler, Thomas Brand Heart Science Centre, National Heart and Lung Institute (NHLI), Imperial College London, United Kingdom article info abstract Article history: Popeye domain containing (Popdc) proteins are a unique family, which combine several different Received 16 September 2015 properties and functions in a surprisingly complex fashion. They are expressed in multiple tissues and Received in revised form cell types, present in several subcellular compartments, interact with different classes of proteins, and 3 December 2015 are associated with a variety of physiological and pathophysiological processes. Moreover, Popdc proteins Accepted 4 January 2016 bind the second messenger cAMP with high affinity and it is thought that they act as a novel class of Available online xxx cAMP effector proteins. Here, we will review the most important findings about the Popdc family, which accumulated since its discovery about 15 years ago. We will be focussing on Popdc protein interaction Keywords: Popeye domain containing genes and function in striated muscle tissue. However, as a full picture only emerges if all aspects are taken into cAMP account, we will also describe what is currently known about the role of Popdc proteins in epithelial cells Proteineprotein interaction and in various types of cancer, and discuss these findings with regard to their relevance for cardiac and Ion channel skeletal muscle. -
Loss-Of-Function Mutation in the Dioxygenase-Encoding FTO Gene
Loss-of-Function Mutation in the Dioxygenase-Encoding FTO Gene Causes Severe Growth Retardation and Multiple Malformations Sarah Boissel, Orit Reish, Karine Proulx, Hiroko Kawagoe-Takaki, Barbara Sedgwick, Giles Yeo, David Meyre, Christelle Golzio, Florence Molinari, Noman Kadhom, et al. To cite this version: Sarah Boissel, Orit Reish, Karine Proulx, Hiroko Kawagoe-Takaki, Barbara Sedgwick, et al.. Loss-of- Function Mutation in the Dioxygenase-Encoding FTO Gene Causes Severe Growth Retardation and Multiple Malformations. American Journal of Human Genetics, Elsevier (Cell Press), 2009, 85 (1), pp.106-111. 10.1016/j.ajhg.2009.06.002. hal-02044723 HAL Id: hal-02044723 https://hal.archives-ouvertes.fr/hal-02044723 Submitted on 21 Feb 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. REPORT Loss-of-Function Mutation in the Dioxygenase-Encoding FTO Gene Causes Severe Growth Retardation and Multiple Malformations Sarah Boissel,1,7 Orit Reish,2,7 Karine Proulx,3,7 Hiroko Kawagoe-Takaki,4 Barbara Sedgwick,4 Giles S.H. Yeo,3 David Meyre,5 Christelle Golzio,1 Florence Molinari,1 Noman Kadhom,1 Heather C. Etchevers,1 Vladimir Saudek,3 I. Sadaf Farooqi,3 Philippe Froguel,5,6 Tomas Lindahl,4 Stephen O’Rahilly,3 Arnold Munnich,1 and Laurence Colleaux1,* FTO is a nuclear protein belonging to the AlkB-related non-haem iron- and 2-oxoglutarate-dependent dioxygenase family. -
Autism Multiplex Family with 16P11.2P12.2 Microduplication Syndrome in Monozygotic Twins and Distal 16P11.2 Deletion in Their Brother
European Journal of Human Genetics (2012) 20, 540–546 & 2012 Macmillan Publishers Limited All rights reserved 1018-4813/12 www.nature.com/ejhg ARTICLE Autism multiplex family with 16p11.2p12.2 microduplication syndrome in monozygotic twins and distal 16p11.2 deletion in their brother Anne-Claude Tabet1,2,3,4, Marion Pilorge2,3,4, Richard Delorme5,6,Fre´de´rique Amsellem5,6, Jean-Marc Pinard7, Marion Leboyer6,8,9, Alain Verloes10, Brigitte Benzacken1,11,12 and Catalina Betancur*,2,3,4 The pericentromeric region of chromosome 16p is rich in segmental duplications that predispose to rearrangements through non-allelic homologous recombination. Several recurrent copy number variations have been described recently in chromosome 16p. 16p11.2 rearrangements (29.5–30.1 Mb) are associated with autism, intellectual disability (ID) and other neurodevelopmental disorders. Another recognizable but less common microdeletion syndrome in 16p11.2p12.2 (21.4 to 28.5–30.1 Mb) has been described in six individuals with ID, whereas apparently reciprocal duplications, studied by standard cytogenetic and fluorescence in situ hybridization techniques, have been reported in three patients with autism spectrum disorders. Here, we report a multiplex family with three boys affected with autism, including two monozygotic twins carrying a de novo 16p11.2p12.2 duplication of 8.95 Mb (21.28–30.23 Mb) characterized by single-nucleotide polymorphism array, encompassing both the 16p11.2 and 16p11.2p12.2 regions. The twins exhibited autism, severe ID, and dysmorphic features, including a triangular face, deep-set eyes, large and prominent nasal bridge, and tall, slender build. The eldest brother presented with autism, mild ID, early-onset obesity and normal craniofacial features, and carried a smaller, overlapping 16p11.2 microdeletion of 847 kb (28.40–29.25 Mb), inherited from his apparently healthy father. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Location Analysis of Estrogen Receptor Target Promoters Reveals That
Location analysis of estrogen receptor ␣ target promoters reveals that FOXA1 defines a domain of the estrogen response Jose´ e Laganie` re*†, Genevie` ve Deblois*, Ce´ line Lefebvre*, Alain R. Bataille‡, Franc¸ois Robert‡, and Vincent Gigue` re*†§ *Molecular Oncology Group, Departments of Medicine and Oncology, McGill University Health Centre, Montreal, QC, Canada H3A 1A1; †Department of Biochemistry, McGill University, Montreal, QC, Canada H3G 1Y6; and ‡Laboratory of Chromatin and Genomic Expression, Institut de Recherches Cliniques de Montre´al, Montreal, QC, Canada H2W 1R7 Communicated by Ronald M. Evans, The Salk Institute for Biological Studies, La Jolla, CA, July 1, 2005 (received for review June 3, 2005) Nuclear receptors can activate diverse biological pathways within general absence of large scale functional data linking these putative a target cell in response to their cognate ligands, but how this binding sites with gene expression in specific cell types. compartmentalization is achieved at the level of gene regulation is Recently, chromatin immunoprecipitation (ChIP) has been used poorly understood. We used a genome-wide analysis of promoter in combination with promoter or genomic DNA microarrays to occupancy by the estrogen receptor ␣ (ER␣) in MCF-7 cells to identify loci recognized by transcription factors in a genome-wide investigate the molecular mechanisms underlying the action of manner in mammalian cells (20–24). This technology, termed 17-estradiol (E2) in controlling the growth of breast cancer cells. ChIP-on-chip or location analysis, can therefore be used to deter- We identified 153 promoters bound by ER␣ in the presence of E2. mine the global gene expression program that characterize the Motif-finding algorithms demonstrated that the estrogen re- action of a nuclear receptor in response to its natural ligand. -
Epigenetic Regulation of the Human Genome by Transposable Elements
EPIGENETIC REGULATION OF THE HUMAN GENOME BY TRANSPOSABLE ELEMENTS A Dissertation Presented to The Academic Faculty By Ahsan Huda In Partial Fulfillment Of the Requirements for the Degree Doctor of Philosophy in Bioinformatics in the School of Biology Georgia Institute of Technology August 2010 EPIGENETIC REGULATION OF THE HUMAN GENOME BY TRANSPOSABLE ELEMENTS Approved by: Dr. I. King Jordan, Advisor Dr. John F. McDonald School of Biology School of Biology Georgia Institute of Technology Georgia Institute of Technology Dr. Leonardo Mariño-Ramírez Dr. Jung Choi NCBI/NLM/NIH School of Biology Georgia Institute of Technology Dr. Soojin Yi, School of Biology Georgia Institute of Technology Date Approved: June 25, 2010 To my mother, your life is my inspiration... ACKNOWLEDGEMENTS I am evermore thankful to my advisor Dr. I. King Jordan for his guidance, support and encouragement throughout my years as a PhD student. I am very fortunate to have him as my mentor as he is instrumental in shaping my personal and professional development. His contributions will continue to impact my life and career and for that I am forever grateful. I am also thankful to my committee members, John McDonald, Leonardo Mariño- Ramírez, Soojin Yi and Jung Choi for their continued support during my PhD career. Through my meetings and discussions with them, I have developed an appreciation for the scientific method and a thorough understanding of my field of study. I am especially grateful to my friends and colleagues, Lee Katz and Jittima Piriyapongsa for their support and presence, which brightened the atmosphere in the lab in the months and years past. -
Supporting Information
Supporting Information Edgar et al. 10.1073/pnas.1601895113 SI Methods (Actimetrics), and recordings were analyzed using LumiCycle Mice. Sample size was determined using the resource equation: Data Analysis software (Actimetrics). E (degrees of freedom in ANOVA) = (total number of exper- – Cell Cycle Analysis of Confluent Cell Monolayers. NIH 3T3, primary imental animals) (number of experimental groups), with −/− sample size adhering to the condition 10 < E < 20. For com- WT, and Bmal1 fibroblasts were sequentially transduced − − parison of MuHV-4 and HSV-1 infection in WT vs. Bmal1 / with lentiviral fluorescent ubiquitin-based cell cycle indicators mice at ZT7 (Fig. 2), the investigator did not know the genotype (FUCCI) mCherry::Cdt1 and amCyan::Geminin reporters (32). of the animals when conducting infections, bioluminescence Dual reporter-positive cells were selected by FACS (Influx Cell imaging, and quantification. For bioluminescence imaging, Sorter; BD Biosciences) and seeded onto 35-mm dishes for mice were injected intraperitoneally with endotoxin-free lucif- subsequent analysis. To confirm that expression of mCherry:: Cdt1 and amCyan::Geminin correspond to G1 (2n DNA con- erin (Promega E6552) using 2 mg total per mouse. Following < ≤ anesthesia with isofluorane, they were scanned with an IVIS tent) and S/G2 (2 n 4 DNA content) cell cycle phases, Lumina (Caliper Life Sciences), 15 min after luciferin admin- respectively, cells were stained with DNA dye DRAQ5 (abcam) and analyzed by flow cytometry (LSR-Fortessa; BD Biosci- istration. Signal intensity was quantified using Living Image ences). To examine dynamics of replicative activity under ex- software (Caliper Life Sciences), obtaining maximum radiance perimental confluent conditions, synchronized FUCCI reporter for designated regions of interest (photons per second per − − − monolayers were observed by time-lapse live cell imaging over square centimeter per Steradian: photons·s 1·cm 2·sr 1), relative 3 d (Nikon Eclipse Ti-E inverted epifluorescent microscope). -
1 UST College of Science Department of Biological Sciences
UST College of Science Department of Biological Sciences 1 Pharmacogenomics of Myofascial Pain Syndrome An Undergraduate Thesis Submitted to the Department of Biological Sciences College of Science University of Santo Tomas In Partial Fulfillment of the Requirements for the Degree of Bachelor of Science in Biology Jose Marie V. Lazaga Marc Llandro C. Fernandez May 2021 UST College of Science Department of Biological Sciences 2 PANEL APPROVAL SHEET This undergraduate research manuscript entitled: Pharmacogenomics of Myofascial Pain Syndrome prepared and submitted by Jose Marie V. Lazaga and Marc Llandro C. Fernandez, was checked and has complied with the revisions and suggestions requested by panel members after thorough evaluation. This final version of the manuscript is hereby approved and accepted for submission in partial fulfillment of the requirements for the degree of Bachelor of Science in Biology. Noted by: Asst. Prof. Marilyn G. Rimando, PhD Research adviser, Bio/MicroSem 602-603 Approved by: Bio/MicroSem 603 panel member Bio/MicroSem 603 panel member Date: Date: UST College of Science Department of Biological Sciences 3 DECLARATION OF ORIGINALITY We hereby affirm that this submission is our own work and that, to the best of our knowledge and belief, it contains no material previously published or written by another person nor material to which a substantial extent has been accepted for award of any other degree or diploma of a university or other institute of higher learning, except where due acknowledgement is made in the text. We also declare that the intellectual content of this undergraduate research is the product of our work, even though we may have received assistance from others on style, presentation, and language expression. -
Transcriptome Sequencing and Genome-Wide Association Analyses Reveal Lysosomal Function and Actin Cytoskeleton Remodeling in Schizophrenia and Bipolar Disorder
Molecular Psychiatry (2015) 20, 563–572 © 2015 Macmillan Publishers Limited All rights reserved 1359-4184/15 www.nature.com/mp ORIGINAL ARTICLE Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder Z Zhao1,6,JXu2,6, J Chen3,6, S Kim4, M Reimers3, S-A Bacanu3,HYu1, C Liu5, J Sun1, Q Wang1, P Jia1,FXu2, Y Zhang2, KS Kendler3, Z Peng2 and X Chen3 Schizophrenia (SCZ) and bipolar disorder (BPD) are severe mental disorders with high heritability. Clinicians have long noticed the similarities of clinic symptoms between these disorders. In recent years, accumulating evidence indicates some shared genetic liabilities. However, what is shared remains elusive. In this study, we conducted whole transcriptome analysis of post-mortem brain tissues (cingulate cortex) from SCZ, BPD and control subjects, and identified differentially expressed genes in these disorders. We found 105 and 153 genes differentially expressed in SCZ and BPD, respectively. By comparing the t-test scores, we found that many of the genes differentially expressed in SCZ and BPD are concordant in their expression level (q ⩽ 0.01, 53 genes; q ⩽ 0.05, 213 genes; q ⩽ 0.1, 885 genes). Using genome-wide association data from the Psychiatric Genomics Consortium, we found that these differentially and concordantly expressed genes were enriched in association signals for both SCZ (Po10 − 7) and BPD (P = 0.029). To our knowledge, this is the first time that a substantially large number of genes show concordant expression and association for both SCZ and BPD. Pathway analyses of these genes indicated that they are involved in the lysosome, Fc gamma receptor-mediated phagocytosis, regulation of actin cytoskeleton pathways, along with several cancer pathways.