Genenames.org: the HGNC and VGNC resources in 2017

Abstract

The HUGO Gene Nomenclature Committee (HGNC) based at the European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. Currently the HGNC database contains almost 40 000 approved gene symbols, over 19 000 of which represent protein-coding genes. In addition to naming genomic loci we manually curate genes into family sets based on shared characteristics such as homology, function or phenotype. We have recently updated our gene family resources and introduced new improved visualizations which can be seen alongside our gene symbol reports on our primary website http://www.genenames.org. In 2016 we expanded our remit and formed the Vertebrate Gene Nomenclature Committee (VGNC) which is responsible for assigning names to vertebrate species lacking a dedicated nomenclature group. Using the chimpanzee genome as a pilot project we have approved symbols and names for over 14 500 protein-coding genes in chimpanzee, and have developed a new website http://vertebrate.genenames.org to distribute these data. Here, we review our online data and resources, focusing particularly on the improvements and new developments made during the last two years.

NET silencing by let-7i in postural tachycardia syndrome

“…Filtered reads were mapped to the human genome using STAR aligner (42). Human genome sequence and version 78 annotations were obtained from the Ensembl FTP site (43). FeatureCounts was used to count reads mapped to exons and generate the expression count matrix (44).…”

Using FlyBase to Find Functionally Related Drosophila Genes

“…The “External Data” section of a Gene Group report includes links to equivalent gene collections at other databases to facilitate cross-organism analyses, notably human gene families at the HGNC, which are also manually compiled and verified [10]. Indeed, the reciprocal links that exist between HGNC gene families and FlyBase Gene Groups should be the primary method to compare related gene sets between humans and D. melanogaster , rather than using the “View Orthologs” option described above.…”

“…For some species (e.g., humans [10]), genes belonging to particular families/groups are given symbols/names with identical prefixes or “root symbols”, meaning that functionally related genes can be retrieved/classified by their nomenclature to some extent. This approach should not be used to identify D. melanogaster gene sets—gene nomenclature is generally not as systematic in this species with many genes given an esoteric symbol/name based on their mutant phenotype.…”

MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome

“…MARRVEL search allows three types of inputs: a single HUGO gene symbol, 28 a single human variant, or a combination of both. The human variant input can be in the format conforming to HGVS nomenclature 29 30 is used to transform the variant input into genomic coordinate, as variants stored in our database follow the genomic variant format.…”