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Genenames.org: the HGNC resources in 2015

Kristian A. Gray, Bethan Yates, Ruth L. Seal, Mathew W. Wright, Elspeth A. Bruford
2014 Nucleic Acids Research  
To date the HGNC have assigned over 39 000 gene names and, representing an increase of over 5000 entries in the past two years.  ...  This article provides an overview of our current online data and resources, and highlights the changes we have made in recent years.  ...  ACKNOWLEDGEMENT The authors would like to thank their former colleagues, specialist advisors and other researchers who have provided invaluable contributions to this project.  ... 
doi:10.1093/nar/gku1071 pmid:25361968 pmcid:PMC4383909 fatcat:6bgwdrhfizcmtfnls2i7s3iwly

Genenames.org: the HGNC and VGNC resources in 2017

Bethan Yates, Bryony Braschi, Kristian A. Gray, Ruth L. Seal, Susan Tweedie, Elspeth A. Bruford
2016 Nucleic Acids Research  
The HUGO Gene Nomenclature Committee (HGNC) based at the European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes.  ...  Here, we review our online data and resources, focusing particularly on the improvements and new developments made during the last two years.  ...  ACKNOWLEDGEMENTS The authors would like to thank their former colleagues, specialist advisors and other researchers for their invaluable contributions to this project.  ... 
doi:10.1093/nar/gkw1033 pmid:27799471 pmcid:PMC5210531 fatcat:4lums3a3tffutdx2wgv77gsoki

A review of the new HGNC gene family resource

Kristian A Gray, Ruth L Seal, Susan Tweedie, Mathew W Wright, Elspeth A Bruford
2016 Human Genomics  
The HUGO Gene Nomenclature Committee (HGNC) approves unique gene symbols and names for human loci.  ...  Each HGNC gene family has its own dedicated gene family report on our website, www.genenames.org.  ...  Funding The work of the HGNC is supported by National Human Genome Research Institute (NHGRI) grant U41HG003345 and Wellcome Trust grant 099129/Z/12/Z. Author details  ... 
doi:10.1186/s40246-016-0062-6 pmid:26842383 pmcid:PMC4739092 fatcat:xyx5vkdkkreqrppfozwsxfw7ja

Front & Back Matter

2015 Cytogenetic and Genome Research  
Providing a wealth of current and archival information on hemiphractid biology and cytogenetics, this monograph is recommended for specialists in the fi elds of zoology, herpetology, embryology and cytogenetics  ...  , as well as for students with an interest in vertebrate cytogenetics.  ...  1SA, UK E-Mail: hgnc@genenames.org Website: Lois Maltais MGD Nomenclature Coordinator The Jackson Laboratory 600 Main Street Bar Harbour, ME 04609, USA Tel.: +1 (207) 288 6429 Fax: +1 (207) 288  ... 
doi:10.1159/000439603 fatcat:epsaolfx3vctvheguj4swqpl6i

Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species

Michelle N. Knowlton, Cynthia L. Smith
2017 Mammalian Genome  
Acknowledgements We would like to thank the following people for their assistance in determining the nomenclature guidelines for different species: Tanya Open Access This article is distributed under  ...  the terms of the Creative Commons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided  ...  In the absence of standard allele nomenclature, several agricultural organisms have adopted guidelines in keeping with HUGO Gene Nomenclature Committee (HGNC) guidelines (http://www. genenames.org/, Yates  ... 
doi:10.1007/s00335-017-9698-3 pmid:28589392 pmcid:PMC5569137 fatcat:leeeruwoy5dwxdg3mqwcbimfui

The official unified nomenclature adopted by the HGNC calls for the use of the acronyms, CCN1–6, and discontinuation in the use of CYR61, CTGF, NOV and WISP 1–3 respectively

Bernard Perbal, Susan Tweedie, Elspeth Bruford
2018 Journal of cell communication and signaling  
After careful consideration of the various arguments, and after polling the community of researchers who have published in the field over the past ten years, the HGNC have decided to adopt and approve  ...  Accordingly, the Journal of Cell Communication and Signaling, the official journal of the International CCN Society, available both in print and online, constitutes a unique window into the CCN field.  ...  Perbal for critical reading of the manuscript.  ... 
doi:10.1007/s12079-018-0491-1 pmid:30393824 pmcid:PMC6235780 fatcat:jxdwfkovs5g75atq25pjz5wjbm

Finding directionality and gene-disease predictions in disease associations

Manuel Garcia-Albornoz, Jens Nielsen
2015 BMC Systems Biology  
Methods: The present study offers the integration of HGNC approved gene symbols, KEGG metabolic pathways andICD-10-CM codes for the analysis of associations based on the level of inclusion and hypergeometricenrichment  ...  Understanding the underlying molecular mechanisms in human diseases is important for diagnosis and treatment of complex conditions and has traditionally been done by establishing associations between disorder-genes  ...  The complete HGNC database can be downloaded from genenames.org (http://www. genenames.org/cgi-bin/statistics).  ... 
doi:10.1186/s12918-015-0184-9 pmid:26168918 pmcid:PMC4501277 fatcat:pava4hqr3faedllzngr3vpyosi

Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials

Marvin Martens, Tim Verbruggen, Penny Nymark, Roland Grafström, Lyle D. Burgoon, Hristo Aladjov, Fernando Torres Andón, Chris T. Evelo, Egon L. Willighagen
2018 Frontiers in Genetics  
A paradigm shift is taking place in risk assessment to replace animal models, reduce the number of economic resources, and refine the methodologies to test the growing number of chemicals and nanomaterials  ...  However, the implementation of omics-based approaches in the AOPs and their acceptance by the risk assessment community is still a challenge.  ...  Committee (HGNC) (HUGO Gene Nomenclature Committee [HGNC] , 2018) in May 2018 via genenames.org, a curated online repository for HGNC-approved gene nomenclature, gene families and associated resources  ... 
doi:10.3389/fgene.2018.00661 pmid:30622555 pmcid:PMC6308971 fatcat:k32w6h6zazg5xhhtj6bulgi3gu

Recent advances in predicting gene–disease associations

Kenneth Opap, Nicola Mulder
2017 F1000Research  
.: Genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 2015; 43(Database issue): D1079-85. PubMed Abstract | Publisher Full Text | Free Full Text 55.  ...  .: The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2014; 42(Database issue): D1001-6.  ...  These facilities encourage adoption of the resource.  ... 
doi:10.12688/f1000research.10788.1 pmid:28529714 pmcid:PMC5414807 fatcat:hzph7zrm55ecje7fsp2yfk66uq

Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways

Maxim Sorokin, Nicolas Borisov, Denis Kuzmin, Alexander Gudkov, Marianna Zolotovskaia, Andrew Garazha, Anton Buzdin
2021 Frontiers in Genetics  
However, different pathway nodes may have different functions toward overall pathway regulation, and calculation of PAL requires knowledge of molecular function of every node in the pathway in terms of  ...  In turn, the pathway activation profiles can characterize molecular processes, which are differentially regulated and give numeric characteristics of the extent of their activation or inhibition.  ...  ACKNOWLEDGMENTS We thank Oncobox/OmicsWay research program in machine learning and digital oncology for software and starting pathway databases for this study.  ... 
doi:10.3389/fgene.2021.617059 pmid:33633781 pmcid:PMC7900570 fatcat:mgfhvafd2jcghldsz7yrmrbooa

Recounting the FANTOM CAGE–Associated Transcriptome

Eddie Luidy Imada, Diego F Sanchez, Leonardo Collado-Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara, Aleksey Stupnikov, Francisco Pereira Pereira Lobo, Chi-Wai Yip, Kayoko Yasuzawa, Naoto Kondo, Masayoshi Itoh (+12 others)
2020 Genome Research  
This atlas greatly extends the gene annotation used in the original recount2 resource.  ...  Our resource is instrumental for the systematic molecular characterization of lncRNA by the FANTOM6 Consortium.  ...  Acknowledgments This publication was made possible through support from the National Institutes of Health-National Cancer Institute (NIH-NCI) grants P30CA006973 (L.M. and A.  ... 
doi:10.1101/gr.254656.119 pmid:32079618 pmcid:PMC7397872 fatcat:rzxz3edayzghdfprs3ger7uk6i

Genetic relationship between Hashimoto`s thyroiditis and papillary thyroid carcinoma with coexisting Hashimoto`s thyroiditis

Ohoud Subhi, Hans-Juergen Schulten, Nadia Bagatian, Roa'a Al-Dayini, Sajjad Karim, Sherin Bakhashab, Reem Alotibi, Alaa Al-Ahmadi, Manar Ata, Aisha Elaimi, Saad Al-Muhayawi, Majid Mansouri (+6 others)
2020 PLoS ONE  
Hashimoto's thyroiditis (HT) is present in the background of around 30% of papillary thyroid carcinomas (PTCs).  ...  deregulated in a data set shared between HT and PTC w/ HT.  ...  Badri, Faculty of Medicine, King Abdulaziz University, for his contribution to the study.  ... 
doi:10.1371/journal.pone.0234566 pmid:32603365 fatcat:pkbcemmhq5h2dgpidhpeuz5cdu

Resources, challenges and way forward in rare mitochondrial diseases research

Neeraj Kumar Rajput, Vipin Singh, Anshu Bhardwaj
2015 F1000Research  
Gray KA, Yates B, Seal RL, et al.: Genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 2015; 43(Database issue): D1079-85. PubMed Abstract | Publisher Full Text 47.  ...  This review focuses on the resources developed over the past years for analysis of genome data towards understanding disease biology especially in the context of mitochondrial diseases, given that mitochondria  ...  The list of various mitochondrial resources may be seen in Table 1 .  ... 
doi:10.12688/f1000research.6208.1 pmid:26180633 pmcid:PMC4490798 fatcat:wkozrz3bjzanhf54gqxirqq3y4

Immediate changes in transcription factors and synaptic transmission in the cochlea following acoustic trauma: a gene transcriptome study

Yukihide Maeda, Shin Kariya, Kensuke Uraguchi, Junko Takahara, Shohei Fujimoto, Akiko Sugaya, Kazunori Nishizaki
2020 Neuroscience research  
The differentially regulated transcription factor Atf3 immunolocalized to supporting cells and hair cells in the organ of Corti at 12-h post-noise.  ...  Pathologic mechanisms in cochleae immediately following the onset of noise-induced hearing loss (NIHL) remain unclear.  ...  Supplementary data Supplementary material related to this article can be found, in the online version, at doi:https://doi.org/10.1016/j.neures.2020.05. 001.  ... 
doi:10.1016/j.neures.2020.05.001 pmid:32417196 fatcat:4avkppcmsbg3rljcifmzkiw7pi

The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY

Simon D Harding, Joanna L Sharman, Elena Faccenda, Chris Southan, Adam J Pawson, Sam Ireland, Alasdair J G Gray, Liam Bruce, Stephen P H Alexander, Stephen Anderton, Clare Bryant, Anthony P Davenport (+5 others)
2017 Nucleic Acids Research  
This update describes content expansion, new features and interoperability improvements introduced in the 10 releases since August 2015.  ...  This resource continues to be developed in conjunction with the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS).  ...  ACKNOWLEDGEMENTS The authors wish to thank all members of NC-IUPHAR for their continued support  ... 
doi:10.1093/nar/gkx1121 pmid:29149325 pmcid:PMC5753190 fatcat:qsfc2kt66vgilah6fwhnpul6we
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