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Journal Article
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Human genetics of face recognition: discovery of MCTP2 mutations in humans with face blindness (Congenital Prosopagnosia) Get access
Yun Sun and others
Genetics, iyae047, https://doi.org/10.1093/genetics/iyae047
Published: 28 March 2024
Journal Article
What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species
Evelina Y Basenko and others
Genetics, iyae035, https://doi.org/10.1093/genetics/iyae035
Published: 26 March 2024
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An overview of new features in FungiDB. New features are grouped into 5 cat...
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Genetics
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What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species
Published: 26 March 2024
Fig. 2.
An overview of new features in FungiDB. New features are grouped into 5 categories: major infrastructure updates, new tools and significant improvements, new searches that facilitate data mining of new or established data types, updates to gene record pages, and the integrated VEuPathDB Galaxy–My Wo
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Site search, search categories, and data filtering. Searching for the term ...
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Genetics
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What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species
Published: 26 March 2024
Fig. 5.
Site search, search categories, and data filtering. Searching for the term “ergosterol” yields a list of results. Gene results are subsequently refined with additional filters within the “Filter Gene Fields” and “Filter Organisms” to identify genes that contain “ergosterol” in the “Product descripti
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Key enrichment analysis tools. The enrichment tools are located under the “...
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Genetics
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What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species
Published: 26 March 2024
Fig. 7.
Key enrichment analysis tools. The enrichment tools are located under the “Analyze Results” tab, which is positioned above the results table. 1) GO Enrichment analysis enriches data on GO terms for molecular function, cellular component, and biological process annotations. 2) The Metabolic Pathway E
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The MGI mouse Pten gene detail page. The mouse gene detail page for Pten sh...
Published: 26 March 2024
Fig. 3.
The MGI mouse Pten gene detail page. The mouse gene detail page for Pten shows the integrated at-a-glance summary information associated with the gene in MGI. Summary data shown here is from MGI's curation pipelines, direct data submissions from researchers and integration of data from a large numbe
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Representation of PARX/PARY partners in MGI. The first two sections of the ...
Published: 26 March 2024
Fig. 4.
Representation of PARX/PARY partners in MGI. The first two sections of the gene detail pages for PARX/PARY partners, G530011O06Rikx and G530011O06Riky are shown. a) Partial gene detail page for G530011O06Rikx . In the Summary section, gene nomenclature has suffix “x”, indicating the feature is
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MGI allele relationships to genetic markers. a) Marker relationships are sh...
Published: 26 March 2024
Fig. 6.
MGI allele relationships to genetic markers. a) Marker relationships are shown in the Mutation Description section of allele detail pages and on allele summary pages. Shown are the Markers related to the deletion mutation Del(2Dlx1-Dlx2)1Jlr curated in MGI. Clicking the “View All” link will open a p
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Connecting phenotypes and genotypes with the MGI SNP Query Form. A common p...
Published: 26 March 2024
Fig. 7.
Connecting phenotypes and genotypes with the MGI SNP Query Form. A common path to the SNP Query Form starts by selecting the Strains, SNPs & Polymorphisms option on the MGI Home Page a), which leads to the Strains and SNPs landing page b), which includes the Strain Query form and various strain-
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Assay detail page for an immunohistochemistry experiment. Only the upper pa...
Published: 26 March 2024
Fig. 10.
Assay detail page for an immunohistochemistry experiment. Only the upper part of the entry is shown. Arrow points to the expression results for specimen S3A, which are annotated in a modular way by combining terms from the anatomy and cell ontology.
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Components of the genome browser JBrowse display. a) The Apollo genome edit...
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Genetics
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What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species
Published: 26 March 2024
Fig. 3.
Components of the genome browser JBrowse display. a) The Apollo genome editor interface. Users can update gene models in the Apollo editor using the underlying data in FungiDB and draggable tracks (indicated by the red box). The revised and completed gene model shown in the “User-created Annotation”
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Creating multistep strategies in FungiDB. a) Example strategy identifying p...
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Genetics
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What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species
Published: 26 March 2024
Fig. 6.
Creating multistep strategies in FungiDB. a) Example strategy identifying putative drug targets in several fungal species. Step 1: identify all genes manually annotated with a disease phenotype in PHI-Base. Step 2: nested RNA-Seq evidence search. The nested strategy consists of 4 steps to identify g
Journal Article
Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse
Richard M Baldarelli and others
Genetics, iyae031, https://doi.org/10.1093/genetics/iyae031
Published: 26 March 2024
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Pseudoautosomal Region (PAR) features in GRCm39. MGV view of the PARX regio...
Published: 26 March 2024
Fig. 2.
Pseudoautosomal Region (PAR) features in GRCm39. MGV view of the PARX region, comparing GRCm39 vs GRCm38 assembly representations of PARX annotations. a) MGV Zoom View showing distal ends of Chr X in the C57BL/6J (GRCm39) (top) and C57BL/6J (GRCm38) (bottom) genomes. PARX features in the C57BL/
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GXD Expression Profile Search. a) Expression Profile query form showing a s...
Published: 26 March 2024
Fig. 11.
GXD Expression Profile Search. a) Expression Profile query form showing a search for genes with expression detected in two structures (forebrain and midbrain) and not detected (or assayed in) two structures (hindbrain and spinal cord). Conditions for each row of the profile are combined with a Boole
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The human–mouse disease connection search and results. a) The upper section...
Published: 26 March 2024
Fig. 13.
The human–mouse disease connection search and results. a) The upper section of the HMDC search tool allows you to select multiple fields to search using either Boolean AND or OR. Shown are two selected search fields, Human Genome Location and Disease or Phenotype Name. The chromosome 10 region spann
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The human–mouse disease connection term matching tool. a) When searching th...
Published: 26 March 2024
Fig. 14.
The human–mouse disease connection term matching tool. a) When searching the HMDC by IDs, multiple IDs in a single field are connected by Boolean OR in the search. Searching by HP IDs returns only human genes and searching by MP IDs returns only mouse genes as the ID search does not go across ontolo
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New data in FungiDB since FungiDB Release 37. a) The organism list in Fungi...
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Genetics
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What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species
Published: 26 March 2024
Fig. 1.
New data in FungiDB since FungiDB Release 37. a) The organism list in FungiDB demonstrates fungal and oomycete organisms currently represented in FungiDB. b) The newly integrated data are categorized based on data type. In 2020, the VEuPathDB platform successfully transitioned to a new database infr
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Core elements of the FungiDB homepage. 1) Banner: it includes 1a) release c...
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Genetics
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What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species
Published: 26 March 2024
Fig. 4.
Core elements of the FungiDB homepage. 1) Banner: it includes 1a) release cycle information on the left, 1b) site search and menus centrally, providing access to nearly all searches, tools, and records in FungiDB, and 1c) account management and social media links on the right. 2) My Organism Prefere
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Components of the gene record pages. a) Links to export genes to baskets, a...
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Genetics
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What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species
Published: 26 March 2024
Fig. 8.
Components of the gene record pages. a) Links to export genes to baskets, add genes to favorites, or download gene data. b) FungiDB's organism summary, user comments, structural or functional updates from Apollo, and direct links to orthologs in prominent model databases. c) Shortcuts to the major g
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