Dog Genome SNP Database
Names
More detailed information about this field from each metasource.
Dog Genome SNP Database
metasource: Fairsharing.org
version: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
DoGSD
metasource: Fairsharing.org
version: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
iDog
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
Names
More detailed information about this field from each metasource.
Dog Genome SNP Database
metasource: Fairsharing.orgversion: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
DoGSD
metasource: Fairsharing.orgversion: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
iDog
metasource: re3data.orgversion: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
Names
More detailed information about this field from each metasource.
Dog Genome SNP Database
metasource: Fairsharing.orgversion: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
DoGSD
metasource: Fairsharing.orgversion: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
iDog
metasource: re3data.orgversion: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
Dog Genome SNP Database (DoGSD) is a data container for the variation information of dog/wolf genomes. It was designed and constructed as an SNPs detector and visualization tool to provide the research community a useful resource for the study of dog's population, evolution, phenotype and life habit.
Description
More detailed information about this field from each metasource.
Dog Genome SNP Database (DoGSD) is a data container for the variation information of dog/wolf genomes. It was designed and constructed as an SNPs detector and visualization tool to provide the research community a useful resource for the study of dog's population, evolution, phenotype and life habit.
metasource: Fairsharing.orgversion: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Dogs have been the dearest friends of humans as guardians, companions and working partners for thousands of years. Since dogs are one of the most thoroughly domesticated animals, this has made them a long-term focus and perfect model for domestication genetics studies. Furthermore, their parallel evolution with humans has facilitated our understanding of human evolution itself. However, currently the most widely used dog single nucleotide polymorphism (SNP) dataset is from dbSNP (build139:ftp://ftp.ncbi.nlm.nih.gov/snp/), where ~80% of the ~2.7M SNPs were called from only two dogs, one Boxer(1) and one Standard Poodle(2). dbSNP only provides a total SNP list, combining SNPs from all samples, and does not have individual lists, which limits its usability in population genetic analysis. The rapid development of Next-Generation Sequencing (NGS) technology has facilitated the generation of massive dog/wolf genome datasets. However, SNP calling from the massive data generated by NGS is very laborious and requires a large amount of computational resources. This situation has promoted us to establish a canidae specific database (DoGSD) that focuses on whole genome SNP data from domesticated dogs and grey wolves. We collected SNPs from 2 unpublished dog/wolf genomes, 3 recently published works (3-5) that used 75 dog/wolf samples and the latest dog SNP dataset (dbSNP139). In total, DoGSD includes 8 grey wolves sampled from the Eurasian continent and America, 34 Chinese indigenous dogs from China, 34 breed dogs representing 5 breeds and 1 Dingo. Dogs from the 5 breeds include 11 German Shepherd dogs (Germany), 10 Kunming dogs (China), 11 Tibetan Mastiffs (China), 1 Belgian Malinois (Belgium), and 1 Basenji (Congo). The 34 Chinese indigenous dogs in our samples represent a key phase in dog domestication and are not included in any existing SNP database. DoGSD provides a powerful SNP retrieval interface that can extract data for each individual sample as well as a non-redundant dataset. SNPs are annotated to integrate information such as SNP-related genes, transcripts, proteins, and allows calculation of allele frequencies. DoGSD functionality includes the ability to search for gene-related synonymous and non-synonymous SNPs. In addition, we incorporate the essential genetic statistics viz. F- statistics (Fst) into DoGSD.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
iDog, an integrated resource for domestic dog (Canis lupus familiaris) and wild canids, provides the worldwide dog research community a variety of data services. This includes Genes, Genomes, SNPs, Breed/Disease Traits, Gene Expressions, Single Cell, Dog-Human Homolog Diseases and Literatures. In addition, iDog provides Online tools for performing genomic data visualization and analyses.
metasource: re3data.orgversion: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
Webpage:
https://ngdc.cncb.ac.cn/idog/Webpage
More detailed information about this field from each metasource.
https://ngdc.cncb.ac.cn/idog/
metasource: re3data.orgversion: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
https://bigd.big.ac.cn/dogsdv2/
metasource: Fairsharing.orgversion: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dogvb.big.ac.cn
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: NGDC Data Usage PolicyLicence name
More detailed information about this field from each metasource.
NGDC Data Usage Policy
metasource: Fairsharing.orgversion: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
other
metasource: re3data.orgversion: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
Licence URL
More detailed information about this field from each metasource.
https://bigd.big.ac.cn/policies
metasource: Fairsharing.orgversion: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
https://ngdc.cncb.ac.cn/mission
metasource: re3data.orgversion: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
Publications:
Publications
More detailed information about this field from each metasource.
DoGSD: the dog and wolf genome SNP database
PMID: 25404132
metasource: Fairsharing.org
version: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
DoGSD: the dog and wolf genome SNP database
PMID: 25404132
metasource: Fairsharing.org
version: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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DoGSD: the dog and wolf genome SNP database
PubMed citations: 56.
56 articles citing: DoGSD: the dog and wolf genome SNP database
The genomic landscape of canine diffuse large B-cell lymphoma identifies distinct subtypes with clinical and therapeutic implications. PMID:35726023
Non-invasive sleep EEG measurement in hand raised wolves. PMID:35697910
Molecular Evolutionary Rate Predicts Intraspecific Genetic Polymorphism and Species-Specific Selection. PMID:35456514
MYO5A Frameshift Variant in a Miniature Dachshund with Coat Color Dilution and Neurological Defects Resembling Human Griscelli Syndrome Type 1. PMID:34680875
Canine tumor mutational burden is correlated with TP53 mutation across tumor types and breeds. PMID:34344882
Deletion of the SELENOP gene leads to CNS atrophy with cerebellar ataxia in dogs. PMID:34339417
Comparison of the oncogenomic landscape of canine and feline hemangiosarcoma shows novel parallels with human angiosarcoma. PMID:34296746
Genomic and Transcriptomic Characterization of Canine Osteosarcoma Cell Lines: A Valuable Resource in Translational Medicine. PMID:34079834
Characterizing the molecular and immune landscape of canine bladder cancer. PMID:34021685
Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches. PMID:33556121
Intronic variant in POU1F1 associated with canine pituitary dwarfism. PMID:33550451
Origins and genetic legacy of prehistoric dogs. PMID:33122379
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PMID:33090996
Genomic diversity and population structure of the Leonberger dog breed. PMID:33054768
The molecular effect of a polymorphic microRNA binding site of Wolfram syndrome 1 gene in dogs. PMID:32723293
Cross-species oncogenic signatures of breast cancer in canine mammary tumors. PMID:32680987
Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer. PMID:32546718
A Preliminary Study to Investigate the Genetic Background of Longevity Based on Whole-Genome Sequence Data of Two Methuselah Dogs. PMID:32373156
ATP2A2 SINE Insertion in an Irish Terrier with Darier Disease and Associated Infundibular Cyst Formation. PMID:32354065
YARS2 Missense Variant in Belgian Shepherd Dogs with Cardiomyopathy and Juvenile Mortality. PMID:32183361
A Missense Variant Affecting the C-Terminal Tail of UNC93B1 in Dogs with Exfoliative Cutaneous Lupus Erythematosus (ECLE). PMID:32028618
CitGVD: a comprehensive database of citrus genomic variations. PMID:32025315
Deciphering the puzzles of dog domestication. PMID:31945812
Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health. PMID:31598383
TSEN54 missense variant in Standard Schnauzers with leukodystrophy. PMID:31584937
Identification of Two Independent COL5A1 Variants in Dogs with Ehlers-Danlos Syndrome. PMID:31546637
A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. PMID:31486122
NME5 frameshift variant in Alaskan Malamutes with primary ciliary dyskinesia. PMID:31479451
Identification of Recurrent Activating HER2 Mutations in Primary Canine Pulmonary Adenocarcinoma. PMID:31431454
Whole-exome and whole-transcriptome sequencing of canine mammary gland tumors. PMID:31413331
AKNA Frameshift Variant in Three Dogs with Recurrent Inflammatory Pulmonary Disease. PMID:31357536
A SIX6 Nonsense Variant in Golden Retrievers with Congenital Eye Malformations. PMID:31207931
Identifying Candidate Druggable Targets in Canine Cancer Cell Lines Using Whole-Exome Sequencing. PMID:31175136
ATP13A2 missense variant in Australian Cattle Dogs with late onset neuronal ceroid lipofuscinosis. PMID:30956123
Bald thigh syndrome in sighthounds-Revisiting the cause of a well-known disease. PMID:30794648
A homozygous missense variant in the alkaline phosphatase gene ALPL is associated with a severe form of canine hypophosphatasia. PMID:30700765
Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma. PMID:30664638
iDog: an integrated resource for domestic dogs and wild canids. PMID:30371881
Database Resources of the BIG Data Center in 2019. PMID:30365034
Collaborating genomic, transcriptomic and microbiomic alterations lead to canine extreme intestinal polyposis. PMID:30018743
The evolutionary history of dogs in the Americas. PMID:29976825
Canine NAPEPLD-associated models of human myelin disorders. PMID:29643404
MKLN1 splicing defect in dogs with lethal acrodermatitis. PMID:29565995
A Nonsense Variant in the ACADVL Gene in German Hunting Terriers with Exercise Induced Metabolic Myopathy. PMID:29491033
A Large Deletion in the NSDHL Gene in Labrador Retrievers with a Congenital Cornification Disorder. PMID:28739597
A SINE Insertion in ATP1B2 in Belgian Shepherd Dogs Affected by Spongy Degeneration with Cerebellar Ataxia (SDCA2). PMID:28620085
Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2. PMID:28552356
GSA: Genome Sequence Archive<sup/> PMID:28387199
DNA methylation patterns of behavior-related gene promoter regions dissect the gray wolf from domestic dog breeds. PMID:28321510
A de novo variant in the ASPRV1 gene in a dog with ichthyosis. PMID:28249031
A Missense Variant in KCNJ10 in Belgian Shepherd Dogs Affected by Spongy Degeneration with Cerebellar Ataxia (SDCA1). PMID:28007838
The BIG Data Center: from deposition to integration to translation. PMID:27899658
PGD: a pangolin genome hub for the research community. PMID:27616775
Genetic mapping of canine fear and aggression. PMID:27503363
Questioning the evidence for a Central Asian domestication origin of dogs. PMID:27099289
Identification of genomic variants putatively targeted by selection during dog domestication. PMID:26754411 - http://dx.doi.org/10.1093/nar/
Tags:
Tags
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genome
metasource: Fairsharing.org
version: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
genome visualization
metasource: Fairsharing.org
version: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
single nucleotide polymorphism
metasource: Fairsharing.org
version: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
model organisms, comparative genomics
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
canidae
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
dog
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
genetics
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
genomics
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
grey wolf
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
Tags
More detailed information about this field from each metasource.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
genome visualization
metasource: Fairsharing.orgversion: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
single nucleotide polymorphism
metasource: Fairsharing.orgversion: FAIRsharing.org: DoGSD; Dog Genome SNP Database; DOI: https://doi.org/10.25504/FAIRsharing.exc0vp; Last edited: March 2, 2020, 6:50 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
model organisms, comparative genomics
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
canidae
metasource: re3data.orgversion: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
dog
metasource: re3data.orgversion: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
genetics
metasource: re3data.orgversion: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
genomics
metasource: re3data.orgversion: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
grey wolf
metasource: re3data.orgversion: re3data.org: iDog; editing status 2022-09-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3DH12 last accessed: 2022-11-04
genome genome visualization single nucleotide polymorphism human and other vertebrate genomes model organisms canidae dog genetics genomics grey wolf
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