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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
The Genetic Basis of Hyaline Fibromatosis Syndrome in Patients from a Consanguineous Background: a Case Series
Youssefian et al. BMC Medical Genetics (2018) 19:87 https://doi.org/10.1186/s12881-018-0581-1 CASE REPORT Open Access The genetic basis of hyaline fibromatosis syndrome in patients from a consanguineous background: a case series Leila Youssefian1,4†, Hassan Vahidnezhad1,2†, Andrew Touati1,3†, Vahid Ziaee5†, Amir Hossein Saeidian1, Sara Pajouhanfar1, Sirous Zeinali2,6 and Jouni Uitto1* Abstract Background: Hyaline fibromatosis syndrome (HFS) is a rare heritable multi-systemic disorder with significant dermatologic manifestations. It is caused by mutations in ANTXR2, which encodes a transmembrane receptor involved in collagen VI regulation in the extracellular matrix. Over 40 mutations in the ANTXR2 gene have been associated with cases of HFS. Variable severity of the disorder in different patients has been proposed to be related to the specific mutations in these patients and their location within the gene. Case presentation: In this report, we describe four cases of HFS from consanguineous backgrounds. Genetic analysis identified a novel homozygous frameshift deletion c.969del (p.Ile323Metfs*14) in one case, the previously reported mutation c.134 T > C (p.Leu45Pro) in another case, and the recurrent homozygous frameshift mutation c.1073dup (p.Ala359Cysfs*13) in two cases. The epidemiology of this latter mutation is of particular interest, as it is a candidate for inhibition of nonsense-mediated mRNA decay. Haplotype analysis was performed to determine the origin of this mutation in this consanguineous cohort, which suggested that it may develop sporadically in different populations. Conclusions: This information provides insights on genotype-phenotype correlations, identifies a previously unreported mutation in ANTXR2, and improves the understanding of a recurrent mutation in HFS. -
Two Novel Mutations in the ANTXR2 Gene in a Chinese Patient Suffering from Hyaline Fibromatosis Syndrome: a Case Report
4004 MOLECULAR MEDICINE REPORTS 18: 4004-4008, 2018 Two novel mutations in the ANTXR2 gene in a Chinese patient suffering from hyaline fibromatosis syndrome: A case report YING GAO1, JINLI BAI2, JIANCAI WANG1 and XIAOYAN LIU1 Departments of 1Dermatology and 2Medical Genetics, Capital Institute of Pediatrics, Peking University Teaching Hospital, Beijing 100020, P.R. China Received October 30, 2017; Accepted March 14, 2018 DOI: 10.3892/mmr.2018.9421 Abstract. Hyaline fibromatosis syndrome (HFS; MIM 228600) Introduction is a rare autosomal recessive disorder characterized by the abnormal growth of hyalinized fibrous tissue at subcutaneous Hyaline fibromatosis syndrome (HFS; OMIM 228600), regions on the scalp, ears and neck. The disease is caused by previously termed juvenile hyaline fibromatosis (JHF) and either a homozygous or compound heterozygous mutation of infantile systemic hyalinosis (ISH), is a rare autosomal reces- the anthrax toxin receptor 2 (ANTXR2) gene. The present sive disorder. The disease is characterized by the abnormal study describes a patient with HFS confirmed by clinical growth of hyalinized fibrous tissue, which commonly affects examination as well as histopathological and genetic analyses. subcutaneous regions on the scalp, ears and neck (1). HFS is Numerous painless and variable‑sized subcutaneous nodules classified into different grades according to its clinical mani- were observed on the scalp, ear, trunk and four extremities festation, resulting from the involvement of different organs; of the patient. With increasing age, the number and size of symptoms may include persistent diarrhea and recurrent the nodules gradually increased in the patient. The patient pulmonary infections (2). HFS is caused by either a homo- additionally presented with severe gingival thickening and zygous or compound heterozygous mutation in the anthrax developed pearly papules on the ears, back and penis foreskin. -
Gene Co-Expression Network Mining Using Graph Sparsification
Gene Co-expression Network Mining Using Graph Sparsification THESIS Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By Jinchao Di Graduate Program in Electrical and Computer Engineering The Ohio State University 2013 Master’s Examination Committee: Dr. Kun Huang, Advisor Dr. Raghu Machiraju Dr. Yuejie Chi ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! Copyright by Jinchao Di 2013 ! ! Abstract Identifying and analyzing gene modules is important since it can help understand gene function globally and reveal the underlying molecular mechanism. In this thesis, we propose a method combining local graph sparsification and a gene similarity measurement method TOM. This method can detect gene modules from a weighted gene co-expression network more e↵ectively since we set a local threshold which can detect clusters with di↵erent densities. In our algorithm, we only retain one edge for each gene, which can generate more balanced gene clusters. To estimate the e↵ectiveness of our algorithm we use DAVID to functionally evaluate the gene list for each module we detect and compare our results with some well known algorithms. The result of our algorithm shows better biological relevance than the compared methods and the number of the meaningful biological clusters is much larger than other methods, implying we discover some previously missed gene clusters. Moreover, we carry out a robustness test by adding Gaussian noise with di↵erent variance to the expression data. We find that our algorithm is robust to noise. We also find that some hub genes considered as important genes could be artifacts. -
Diagnosis Implications of the Whole Genome Sequencing in a Large Lebanese Family with Hyaline Fibromatosis Syndrome
Haidar et al. BMC Genetics (2017) 18:3 DOI 10.1186/s12863-017-0471-0 RESEARCHARTICLE Open Access Diagnosis implications of the whole genome sequencing in a large Lebanese family with hyaline fibromatosis syndrome Zahraa Haidar1, Ramzi Temanni2, Eliane Chouery1 , Puthen Jithesh2, Wei Liu3, Rashid Al-Ali2, Ena Wang3, Francesco M Marincola4, Nadine Jalkh1, Soha Haddad5, Wassim Haidar6, Lotfi Chouchane7 and André Mégarbané8* Abstract Background: Hyaline fibromatosis syndrome (HFS) is a recently introduced alternative term for two disorders that were previously known as juvenile hyaline fibromatosis (JHF) and infantile systemic hyalinosis (ISH). These two variants are secondary to mutations in the anthrax toxin receptor 2 gene (ANTXR2) located on chromosome 4q21. The main clinical features of both entities include papular and/or nodular skin lesions, gingival hyperplasia, joint contractures and osteolytic bone lesions that appear in the first few years of life, and the syndrome typically progresses with the appearance of new lesions. Methods: We describe five Lebanese patients from one family, aged between 28 and 58 years, and presenting with nodular and papular skin lesions, gingival hyperplasia, joint contractures and bone lesions. Because of the particular clinical features and the absence of a clinical diagnosis, Whole Genome Sequencing (WGS) was carried out on DNA samples from the proband and his parents. Results: A mutation in ANTXR2 (p. Gly116Val) that yielded a diagnosis of HFS was noted. Conclusions: The main goal of this paper is to add to the knowledge related to the clinical and radiographic aspects of HFS in adulthood and to show the importance of Next-Generation Sequencing (NGS) techniques in resolving such puzzling cases. -
Download Special Issue
BioMed Research International Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data Guest Editors: Julia Tzu-Ya Weng, Li-Ching Wu, Wen-Chi Chang, Tzu-Hao Chang, Tatsuya Akutsu, and Tzong-Yi Lee Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data BioMed Research International Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data Guest Editors: Julia Tzu-Ya Weng, Li-Ching Wu, Wen-Chi Chang, Tzu-Hao Chang, Tatsuya Akutsu, and Tzong-Yi Lee Copyright © 2014 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “BioMed Research International.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Contents Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data,JuliaTzu-YaWeng, Li-Ching Wu, Wen-Chi Chang, Tzu-Hao Chang, Tatsuya Akutsu, and Tzong-Yi Lee Volume2014,ArticleID814092,3pages Evolution of Network Biomarkers from Early to Late Stage Bladder Cancer Samples,Yung-HaoWong, Cheng-Wei Li, and Bor-Sen Chen Volume 2014, Article ID 159078, 23 pages MicroRNA Expression Profiling Altered by Variant Dosage of Radiation Exposure,Kuei-FangLee, Yi-Cheng Chen, Paul Wei-Che Hsu, Ingrid Y. Liu, and Lawrence Shih-Hsin Wu Volume2014,ArticleID456323,10pages EXIA2: Web Server of Accurate and Rapid Protein Catalytic Residue Prediction, Chih-Hao Lu, Chin-Sheng -
ANTXR2 Is a Potential Causative Gene in the Genome-Wide Association Study of the Blood Pressure Locus 4Q21
Hypertension Research (2014) 37, 811–817 & 2014 The Japanese Society of Hypertension All rights reserved 0916-9636/14 www.nature.com/hr ORIGINAL ARTICLE ANTXR2 is a potential causative gene in the genome-wide association study of the blood pressure locus 4q21 So Yon Park1,Hyeon-JuLee1, Su-Min Ji1, Marina E Kim2, Baigalmaa Jigden3, Ji Eun Lim3 and Bermseok Oh1,2,3 Hypertension is the most prevalent cardiovascular disease worldwide, but its genetic basis is poorly understood. Recently, genome-wide association studies identified 33 genetic loci that are associated with blood pressure. However, it has been difficult to determine whether these loci are causative owing to the lack of functional analyses. Of these 33 genome-wide association studies (GWAS) loci, the 4q21 locus, known as the fibroblast growth factor 5 (FGF5) locus, has been linked to blood pressure in Asians and Europeans. Using a mouse model, we aimed to identify a causative gene in the 4q21 locus, in which four genes (anthrax toxin receptor 2 (ANTXR2), PR domain-containing 8 (PRDM8), FGF5 and chromosome 4 open reading frame 22 (C4orf22)) were near the lead single-nucleotide polymorphism (rs16998073). Initially, we examined Fgf5 gene by measuring blood pressure in Fgf5-knockout mice. However, blood pressure did not differ between Fgf5 knockout and wild-type mice. Therefore, the other candidate genes were studied by in vivo small interfering RNA (siRNA) silencing in mice. Antxr2 siRNA was pretreated with polyethylenimine and injected into mouse tail veins, causing a significant decrease in Antxr2 mRNA by 22% in the heart. Moreover, blood pressure measured under anesthesia in Antxr2 siRNA-injected mice rose significantly compared with that of the controls. -
Protective Antigen Complexes with Increased Stability and Uses Thereof
I 1111111111111111 1111111111 1111111111 1111111111 11111 11111 lll111111111111111 US010188716B2 c12) United States Patent (IO) Patent No.: US 10,188,716 B2 Bann et al. (45) Date of Patent: Jan.29,2019 (54) PROTECTIVE ANTIGEN COMPLEXES Williams et al (Protein Science. 2009. 18: 2277-2286).* WITH INCREASED STABILITY AND USES Chadegani, Fatemeh, et al., F Nuclear Magnetic Resonance and THEREOF Crystallographic Studies of 5-Fluorotryptophan-Labeled Anthrax Protective Antigen and Effects of the Receptor on Stability, Copyright (71) Applicants:Wichita State University, Wichita, KS 2014 American Chemical Society, Open Access on Jan. 3, 2015, (US); Case Western Reserve Biochemistry 2014, 53, 690-701 (12 pages). University, Cleveland, OH (US) Wimalasena, D. Shyamili et al, Evidence That Histidine Protonation of Receptor-Bound Anthrax Protective Antigen is a Trigger for Pore (72) Inventors: James G. Bann, Wichita, KS (US); Formation, Biochemistry, 2010, 49 (33), pp. 6973-6983, DOI: Masaru Miyagi, Cleveland, OH (US) 10.1021/bil00647z, Publication Date (Web): Jul. 22, 2010, Copyright © 2010 American Chemical Society (11 pages). (73) Assignees: Wichita State University, Wichita, KS Rajapaksha, Maheshinie et al., pH effects on binding between the (US); Case Western Reserve anthrax protective antigen and the host cellular receptor CMG2, University, Cleveland, OH (US) Protein Science: A Publication ofthe Protein Society.2012;21( 10): 1467- 1480. doi: 10.1002/pro.2136 (14 pages). ( *) Notice: Subject to any disclaimer, the term ofthis Williams, Alexander S et al., Domain 4 of the anthrax protective patent is extended or adjusted under 35 antigen maintains structure and binding to the host receptor CMG2 U.S.C. 154(b) by O days. -
Identification of Significant Genes with Poor Prognosis in Ovarian Cancer Via Bioinformatical Analysis
Feng et al. Journal of Ovarian Research (2019) 12:35 https://doi.org/10.1186/s13048-019-0508-2 RESEARCH Open Access Identification of significant genes with poor prognosis in ovarian cancer via bioinformatical analysis Hao Feng1†, Zhong-Yi Gu2†, Qin Li2, Qiong-Hua Liu3, Xiao-Yu Yang4* and Jun-Jie Zhang2* Abstract Ovarian cancer (OC) is the highest frequent malignant gynecologic tumor with very complicated pathogenesis. The purpose of the present academic work was to identify significant genes with poor outcome and their underlying mechanisms. Gene expression profiles of GSE36668, GSE14407 and GSE18520 were available from GEO database. There are 69 OC tissues and 26 normal tissues in the three profile datasets. Differentially expressed genes (DEGs) between OC tissues and normal ovarian (OV) tissues were picked out by GEO2R tool and Venn diagram software. Next, we made use of the Database for Annotation, Visualization and Integrated Discovery (DAVID) to analyze Kyoto Encyclopedia of Gene and Genome (KEGG) pathway and gene ontology (GO). Then protein-protein interaction (PPI) of these DEGs was visualized by Cytoscape with Search Tool for the Retrieval of Interacting Genes (STRING). There were total of 216 consistently expressed genes in the three datasets, including 110 up-regulated genes enriched in cell division, sister chromatid cohesion, mitotic nuclear division, regulation of cell cycle, protein localization to kinetochore, cell proliferation and Cell cycle, progesterone-mediated oocyte maturation and p53 signaling pathway, while 106 down-regulated genes enriched in palate development, blood coagulation, positive regulation of transcription from RNA polymerase II promoter, axonogenesis, receptor internalization, negative regulation of transcription from RNA polymerase II promoter and no significant signaling pathways. -
Cancer Sequencing Service Data File Formats File Format V2.4 Software V2.4 December 2012
Cancer Sequencing Service Data File Formats File format v2.4 Software v2.4 December 2012 CGA Tools, cPAL, and DNB are trademarks of Complete Genomics, Inc. in the US and certain other countries. All other trademarks are the property of their respective owners. Disclaimer of Warranties. COMPLETE GENOMICS, INC. PROVIDES THESE DATA IN GOOD FAITH TO THE RECIPIENT “AS IS.” COMPLETE GENOMICS, INC. MAKES NO REPRESENTATION OR WARRANTY, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR USE, OR ANY OTHER STATUTORY WARRANTY. COMPLETE GENOMICS, INC. ASSUMES NO LEGAL LIABILITY OR RESPONSIBILITY FOR ANY PURPOSE FOR WHICH THE DATA ARE USED. Any permitted redistribution of the data should carry the Disclaimer of Warranties provided above. Data file formats are expected to evolve over time. Backward compatibility of any new file format is not guaranteed. Complete Genomics data is for Research Use Only and not for use in the treatment or diagnosis of any human subject. Information, descriptions and specifications in this publication are subject to change without notice. Copyright © 2011-2012 Complete Genomics Incorporated. All rights reserved. RM_DFFCS_2.4-01 Table of Contents Table of Contents Preface ...........................................................................................................................................................................................1 Conventions ................................................................................................................................................................................................. -
Rabbit Anti-COPS3/FITC Conjugated Antibody-SL23085R-FITC
SunLong Biotech Co.,LTD Tel: 0086-571- 56623320 Fax:0086-571- 56623318 E-mail:[email protected] www.sunlongbiotech.com Rabbit Anti-COPS3/FITC Conjugated antibody SL23085R-FITC Product Name: Anti-COPS3/FITC Chinese Name: FITC标记的COP9信号复合体亚基3抗体 COP9 Signalosome Complex Subunit 3; CSN10; JAB1 Containing Signalosome Alias: Subunit 3; SGN3; Signalosome Subunit 3; CSN3_HUMAN. Organism Species: Rabbit Clonality: Polyclonal React Species: ICC=1:50-200IF=1:50-200 Applications: not yet tested in other applications. optimal dilutions/concentrations should be determined by the end user. Molecular weight: 48kDa Form: Lyophilized or Liquid Concentration: 2mg/1ml immunogen: KLH conjugated synthetic peptide derived from human COPS3 Lsotype: IgG Purification: affinity purified by Protein A Storage Buffer: 0.01M TBS(pH7.4) with 1% BSA, 0.03% Proclin300 and 50% Glycerol. Storewww.sunlongbiotech.com at -20 °C for one year. Avoid repeated freeze/thaw cycles. The lyophilized antibody is stable at room temperature for at least one month and for greater than a year Storage: when kept at -20°C. When reconstituted in sterile pH 7.4 0.01M PBS or diluent of antibody the antibody is stable for at least two weeks at 2-4 °C. background: The protein encoded by this gene possesses kinase activity that phosphorylates regulators involved in signal transduction. It phosphorylates I kappa-Balpha, p105, and c-Jun. It acts as a docking site for complex-mediated phosphorylation. The gene is Product Detail: located within the Smith-Magenis syndrome region on chromosome 17. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]. -
Downloaded Per Proteome Cohort Via the Web- Site Links of Table 1, Also Providing Information on the Deposited Spectral Datasets
www.nature.com/scientificreports OPEN Assessment of a complete and classifed platelet proteome from genome‑wide transcripts of human platelets and megakaryocytes covering platelet functions Jingnan Huang1,2*, Frauke Swieringa1,2,9, Fiorella A. Solari2,9, Isabella Provenzale1, Luigi Grassi3, Ilaria De Simone1, Constance C. F. M. J. Baaten1,4, Rachel Cavill5, Albert Sickmann2,6,7,9, Mattia Frontini3,8,9 & Johan W. M. Heemskerk1,9* Novel platelet and megakaryocyte transcriptome analysis allows prediction of the full or theoretical proteome of a representative human platelet. Here, we integrated the established platelet proteomes from six cohorts of healthy subjects, encompassing 5.2 k proteins, with two novel genome‑wide transcriptomes (57.8 k mRNAs). For 14.8 k protein‑coding transcripts, we assigned the proteins to 21 UniProt‑based classes, based on their preferential intracellular localization and presumed function. This classifed transcriptome‑proteome profle of platelets revealed: (i) Absence of 37.2 k genome‑ wide transcripts. (ii) High quantitative similarity of platelet and megakaryocyte transcriptomes (R = 0.75) for 14.8 k protein‑coding genes, but not for 3.8 k RNA genes or 1.9 k pseudogenes (R = 0.43–0.54), suggesting redistribution of mRNAs upon platelet shedding from megakaryocytes. (iii) Copy numbers of 3.5 k proteins that were restricted in size by the corresponding transcript levels (iv) Near complete coverage of identifed proteins in the relevant transcriptome (log2fpkm > 0.20) except for plasma‑derived secretory proteins, pointing to adhesion and uptake of such proteins. (v) Underrepresentation in the identifed proteome of nuclear‑related, membrane and signaling proteins, as well proteins with low‑level transcripts.