Genenames.org: the HGNC and VGNC resources in 2021

Tweedie, Susan; Braschi, Bryony; Gray, Kristian; Jones, Tamsin E. M.; Seal, Ruth L.; Yates, Bethan; Bruford, Elspeth A.

doi:10.1093/nar/gkaa980

Cited by 300 publications

(265 citation statements)

References 32 publications

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“…The automated process on free-text content assumes good practice in writing gene symbols and names according to the HGNC guidelines [51]. Although HGNC strives for stable gene symbols and makes justified changes for problematic ones [52], some gene symbols still overlap with free-text abbreviations in the AOP-Wiki and are therefore falsely recognised.…”

Section: Discussionmentioning

confidence: 99%

Providing Adverse Outcome Pathways from the AOP-Wiki in Semantic Web Format to Increase Usability and Accessibility of the Content

Martens

Evelo²,

Willighagen³

2021

Preprint

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<div>The AOP-Wiki is the main environment for the development and storage of Adverse Outcome Pathways. These Adverse Outcome Pathways describe mechanistic information about toxicodynamic processes and can be used to develop effective risk assessment strategies. However, it is challenging to automatically and systematically parse, filter, and use its contents. We explored solutions to better structure the AOP-Wiki content and to link it with chemical and biological resources. Together this allows more detailed exploration which can be automated.</div><div><br></div><div>We converted the complete AOP-Wiki content into Resource Description Framework. We used over twenty ontologies for the semantic annotation of property-object relations, including the ChemInformatics Ontology, Dublin Core, and the Adverse Outcome Pathway Ontology. The latter was used over 8,000 times. Furthermore, over 3,500 link-outs were added to twelve chemical databases and over 6,500 link-outs to four gene and protein databases. </div><div><br></div><div>SPARQL queries can be used against the Resource Description Framework to answer biological and toxicological questions, such as listing measurement methods for all Key Events leading to an Adverse Outcome of interest. The full power that the use of this new resource provides becomes apparent when combining the content with external databases using federated queries. For example, we can link genes related to Key Events with molecular pathway on WikiPathways in which they occur and find all Adverse Outcome Pathways caused by stressors that are part of a particular chemical group. Overall, the AOP-Wiki Resource Description Framework allows new ways to explore the rapidly growing Adverse Outcome Pathway knowledge and makes the integration of this database in automated workflows possible.</div>

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Section: Discussionmentioning

confidence: 99%

Providing Adverse Outcome Pathways from the AOP-Wiki in Semantic Web Format to Increase Usability and Accessibility of the Content

Martens

Evelo²,

Willighagen³

2021

Preprint

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“…We reviewed databases ClinVar ( Landrum et al, 2018 ), LOVD ( Fokkema et al, 2011 ), HGMD ( Stenson et al, 2003 ), COSMIC ( Tate et al, 2019 ), and CIViC ( Griffith et al, 2017 ) to search for clinically relevant data of variants. Gene abbreviations are according to the official symbols in HUGO Gene Nomenclature Committee ( Tweedie et al, 2021 ). The purpose of the reference DNA sample was to serve as a control for sequencing performance.…”

Section: Methodsmentioning

confidence: 99%

Identification of Variants Associated With Rare Hematological Disorder Erythrocytosis Using Targeted Next-Generation Sequencing Analysis

Kristan

Pajič²,

Maver³

et al. 2021

Front. Genet.

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An erythrocytosis is present when the red blood cell mass is increased, demonstrated as elevated hemoglobin and hematocrit in the laboratory evaluation. Congenital predispositions for erythrocytosis are rare, with germline variants in several genes involved in oxygen sensing (VHL, EGLN1, and EPAS1), signaling for hematopoietic cell maturation (EPOR and EPO), and oxygen transfer (HBB, HBA1, HBA2, and BPGM) that were already associated with the eight congenital types (ECYT1–8). Screening for variants in known congenital erythrocytosis genes with classical sequencing approach gives a correct diagnosis for only up to one-third of the patients. The genetic background of erythrocytosis is more heterogeneous, and additional genes involved in erythropoiesis and iron metabolism could have a putative effect on the development of erythrocytosis. This study aimed to detect variants in patients with yet unexplained erythrocytosis using the next-generation sequencing (NGS) approach, targeting genes associated with erythrocytosis and increased iron uptake and implementing the diagnostics of congenital erythrocytosis in Slovenia. Selected 25 patients with high hemoglobin, high hematocrit, and no acquired causes were screened for variants in the 39 candidate genes. We identified one pathogenic variant in EPAS1 gene and three novel variants with yet unknown significance in genes EPAS1, JAK2, and SH2B3. Interestingly, a high proportion of patients were heterozygous carriers for two variants in HFE gene, otherwise pathogenic for the condition of iron overload. The association between the HFE variants and the development of erythrocytosis is not clearly understood. With a targeted NGS approach, we determined an actual genetic cause for the erythrocytosis in one patient and contributed to better management of the disease for the patient and his family. The effect of variants of unknown significance on the enhanced production of red blood cells needs to be further explored with functional analysis. This study is of great significance for the improvement of diagnosis of Slovenian patients with unexplained erythrocytosis and future research on the etiology of this rare hematological disorder.

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“…Moreover, all the couples that were not recognized as paralogues in the current version of the Ensembl database were excluded. To ensure full compatibility among all of the datasets employed, we updated the gene names to the latest officially accepted version -data about the status of gene names were obtained from the HGNC online service (27). Finally, only protein-coding genes (according to the Ensembl database) were considered in our list of paralogues.…”

Section: Methodsmentioning

confidence: 99%

The impact of whole genome duplications on the human gene regulatory networks

Mottes

Villa

Osella

et al. 2021

Preprint

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This work studies the effects of the two rounds of Whole Genome Duplication (WGD) at the origin of the vertebrate lineage on the architecture of the human gene regulatory networks. We integrate information on transcriptional regulation, miRNA regulation, and protein-protein interactions to comparatively analyse the role of WGD and Small Scale Duplications (SSD) in the structural properties of the resulting multilayer network. We show that complex network motifs, such as combinations of feed-forward loops and bifan arrays, deriving from WGD events are specifically enriched in the network. Pairs of WGD-derived proteins display a strong tendency to interact both with each other and with common partners and WGD-derived transcription factors play a prominent role in the retention of a strong regulatory redundancy. Combinatorial regulation and synergy between different regulatory layers are in general enhanced by duplication events, but the two types of duplications contribute in different ways. Overall, our findings suggest that the two WGD events played a substantial role in increasing the multi-layer complexity of the vertebrate regulatory network by enhancing its combinatorial organization, with potential consequences on its overall robustness and ability to perform high-level functions like signal integration and noise control.

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Genenames.org: the HGNC and VGNC resources in 2021

Cited by 300 publications

References 32 publications

Providing Adverse Outcome Pathways from the AOP-Wiki in Semantic Web Format to Increase Usability and Accessibility of the Content

Providing Adverse Outcome Pathways from the AOP-Wiki in Semantic Web Format to Increase Usability and Accessibility of the Content

Identification of Variants Associated With Rare Hematological Disorder Erythrocytosis Using Targeted Next-Generation Sequencing Analysis

The impact of whole genome duplications on the human gene regulatory networks

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