GeneCards Suite Version 5.15 -- 出炉

[Tlexander]

Announcing GeneCards Suite Version 5.15

We are happy to announce the release of GeneCards v5.15 and MalaCards v5.15. This version includes an important improvement to our search functionality, as well as improvements to gene-disease associations.

GeneCards v5.15

The new version includes the following new features and changes:
• 415,866 Entries, 43,617 HGNC approved, 21,667 Protein coding, 292,110 RNA genes including 130,578 lncRNAs, 111,811 piRNAs, and 49,721 other ncRNAs.
• Sample Gene: Our sample gene this version celebrates TYK2, whose variants have recently been shown to be protective against severe COVID-19 but to also increase the risk of auto-immune disease.
• Search within a gene: A new Search in Gene button, on the right side of the header of each GeneCard, enables users to search for a term within all of the gene’s fully expanded data, including information not shown by default on the page, and available via “see all”.
• Search results:
o filtering: By default, search results display hits in all of the matched sections of the GeneCard. In order to focus on key details of interest amongst large amounts of provided information, users can now choose to pinpoint the results to show only selected sections of the card, as shown in the Search Guide.
o query reframing option: When multiple words are specified without quotations, the results page (in addition to providing the hits found by applying the AND operator to the specified terms) now also presents a “Did you mean: ...” option to quote the string and offer a corresponding exact-match query instead.
• Gene-Disease associations: New two-table breakdown of the Disorders section’s MalaCards gene-disease association matrix. The first table contains only diseases found to be directly related to the gene. The second table contains additional diseases, which are inferred to be associated with the gene by one or more text-mining-based sources (see HEXA).
• RNAcentral’s LitScan: Relevant articles provided by RNAcentral’s LitScan text-mining platform are now incorporated into the Publications section (see TERC).
• Variants: Improved data model, which unifies variations using UniProt’s Human Genome Variation Society (HGVS) mapping to ClinVar’s, with links from the renamed Accession column; added new rsID, Ref/Alt. and Amino Acid change columns; split Type values to multiple rows; added more details to the search’s index (e.g. “p.Val411Leu” and “V411L”) (see UGT1A1).
• Exons in Transcripts section: Added a new Exon structure subsection at the bottom of the Transcripts section, which provides a link to a popup with up-to-date GeneLoc Exon structure information (see H19).
• Three dimensional structures: The PDB ID column in the Protein section’s 3D structure table has been replaced with 3 columns - Identifier, Method, and Resolution. In addition, predicted structures from AlphaFold are now included in this table, with the Identifier column’s ID linked to AlphaFold, and the Method column's value set to Predicted (see MTHFR).
• The User Guide has been updated to reflect improvements to the site.
• Data: Updates and/or presentation improvements for a variety of sources including Abcam, Alomone, Aminode, Applied Biological Materials, Applied Biosystems by Thermo Fisher Scientific, ATLAS, Bgee, Biorbyt, BPS Biosciences, CDC, CIViC, CladeOScope, ClinVar, COMPARTMENTS, Cyagen, CUSABIO, dbSNP, DGIdb, DGV, DISEASES, DiseaseEnhancer, DrugBank, ENCODE, Ensembl, EPDnew, FANTOM5, FineTest, Gene ORGANizer, Origene, GeneLoc, GlyGen, GO, GWAS, HGNC, HMDB, HPA, HPO, Humsavar, Invitrogen by ThermoFisher, InVivo Biosystems, Lipexogen, LOVD, MalaCards, Mastermind, MedChemExpress, MGD, MINT, miR2Disease, MIRTARBASE, NCBI Entrez Gene, NOVUS, ODiseA, OMIM, Orphanet, PharmGKB, PharmVar, ProSci, PubMed, PubChem, R&D Systems, Reactome, RNAcentral, Rockland, SGD, SIGNOR, Sino Biological, TISSUES, UCNEbase, UCSC, UDN, UniProt, VectorBuilder, VISTA, WikiPathways.
• Bug fixes; infrastructure, performance and cosmetic improvements



MalaCards v5.15
The new version includes the following new features and changes:
• Upgraded disease list: 22,180 entries, 14,709 with associated genes, consolidated from 75 sources
• Sample disease: Our sample disease this version (see Lymphoproliferative Syndrome, X-Linked, 1 (XLP1)) presents a disease elitely associated with the GeneCards TYK2 sample gene, with evidence provided in the Genes, Related Diseases, Pathways, and Go Terms/Biological processes sections of the MalaCard.
• Updates for a variety of sources including CDC, ClinicalTrials, ClinVar, Disease Ontology, Diseases, EFO, GARD, GeneCards, HPO, ICD, MedGen, MedlinePlus, NINDS, ODiseA, OMIM, Orphanet, PubMed, Reactome, UniProtKB Human diseases, Wikipedia
• Bug fixes