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Alignment of Reactome disease variant annotations with ACMG/AMP-specified c...
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Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Published: 07 May 2024
Figure 6.
Alignment of Reactome disease variant annotations with ACMG/AMP-specified criteria. (A) PS3 variants are annotated as members of disease variant sets. Cancer variant p16INK4 A20P, unable to bind to and inhibit cyclin-dependent kinases CDK4 and CDK6, is annotated as a member of the ‘p16INK4A LoF muta
Journal Article
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Database, Volume 2024, 2024, baae031, https://doi.org/10.1093/database/baae031
Published: 07 May 2024
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Disease variant-associated disease reactions in Reactome pathway diagrams. ...
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Database
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Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Published: 07 May 2024
Figure 2.
Disease variant-associated disease reactions in Reactome pathway diagrams. (A) Automated overlay of a LOF reaction ‘Defective DAXX does not bind ATRX’ (upper panel) onto normal reaction ‘ATRX binds DAXX’ (bottom panel) ( 28 ). (B) Automated overlay of GOF reactions showing phosphorylation of nuclear
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Overlap of Reactome disease variant genes with (A) COSMIC Cancer Gene Censu...
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Database
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Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Published: 07 May 2024
Figure 5.
Overlap of Reactome disease variant genes with (A) COSMIC Cancer Gene Census genes, (B) OMIM disease genes, (C) ClinGen disease genes and (D) COSMIC, OMIM and ClinGen combined. Overlapping COSMIC/Reactome, ClinGen/Reactome and COSMIC/ClinGen/OMIM/Reactome genes are shown. A single disease gene prese
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Pipeline for determining the scope of Reactome disease variant curation. Cl...
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Database
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Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Published: 07 May 2024
Figure 1.
Pipeline for determining the scope of Reactome disease variant curation. ClinGen is shown with dashed borders as it is still to be routinely incorporated in the pipeline.
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Reactome pathway enrichment analysis results shown in the Reactome Voronoi ...
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Database
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Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Published: 07 May 2024
Figure 3.
Reactome pathway enrichment analysis results shown in the Reactome Voronoi map for 372 disease variant genes based on Reactome Release 84.
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Reactome cross-references to DO branches with most frequently cross-referen...
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Database
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Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Published: 07 May 2024
Figure 4.
Reactome cross-references to DO branches with most frequently cross-referenced terms for each branch shown. Labeled large nodes and small unlabeled nodes of the same hue are DO terms annotated in the context of Reactome disease variants. Small unlabeled nodes of a different hue are linker nodes, con
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High-level graphical summary of Reactome’s ERBB2 cancer variants content. (...
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Database
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Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Published: 07 May 2024
Figure 7.
High-level graphical summary of Reactome’s ERBB2 cancer variants content. (A) Heatmap representation of Reactome electronic textbook knowledge on the sensitivity of different ERBB2 cancer variants to ERBB2-targeted anti-cancer therapeutics. The heatmap was generated using the R package pheatmap with
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Data distribution for the six types of cancer immunity. In the figure, the ...
Published: 06 May 2024
Figure 3.
Data distribution for the six types of cancer immunity. In the figure, the horizontal axis represents six types of cancer immunotherapy and the vertical axis represents the quantity. The three bars for each therapy, from left to right, indicate approved therapies, therapies in clinical trials and th
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The analysis page of the database website. From left to right, the first fi...
Published: 06 May 2024
Figure 4.
The analysis page of the database website. From left to right, the first figure shows the ‘Predict you want’ fast predictive interaction interface in the middle and the display of ICIs at the bottom. Figure two shows schematic diagram of the network analysis results and corresponding data table info
Journal Article
DIRMC: a database of immunotherapy-related molecular characteristics
Database, Volume 2024, 2024, baae032, https://doi.org/10.1093/database/baae032
Published: 06 May 2024
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Flowchart of the DIRMC database. From left to right, there are three sectio...
Published: 06 May 2024
Figure 1.
Flowchart of the DIRMC database. From left to right, there are three sections: data sources, data processing and the final database structure, including six types of immunotherapy developed, MHC–peptide and peptide–TCR binding affinity prediction and the reliability scoring system established. The d
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Reliability criteria for interactions in ACTs. Reliability is increasing fr...
Published: 06 May 2024
Figure 2.
Reliability criteria for interactions in ACTs. Reliability is increasing from Levels 1 to 5, with each level having its own judgment criteria.
Journal Article
Correction to: ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides
Database, Volume 2024, 2024, baae035, https://doi.org/10.1093/database/baae035
Published: 06 May 2024
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Cell line details page for HeLa. Derived cell lines and information on the ...
Published: 30 April 2024
Figure 1.
Cell line details page for HeLa. Derived cell lines and information on the cell line donor are listed on this page. The count of associated samples and link to ‘Search Form’ are also shown. The last link on the page redirects to cell line page on Cellosaurus.
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Comparison of copy number sample numbers in cell lines and their origins fo...
Published: 30 April 2024
Figure 2.
Comparison of copy number sample numbers in cell lines and their origins for the most common cancer types. Twenty most common cancer types (by the number of sample count, excluding ‘Unspecified Tissue’ samples) were picked from Progenetix. Cancer types without any cell lines were excluded as well. H
Journal Article
cancercelllines.org—a novel resource for genomic variants in cancer cell lines
Database, Volume 2024, 2024, baae030, https://doi.org/10.1093/database/baae030
Published: 30 April 2024
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Genomic CNV frequencies comparing cancer-type specific profiles to those fr...
Published: 30 April 2024
Figure 3.
Genomic CNV frequencies comparing cancer-type specific profiles to those from selected cell lines for copy number gains (up) and losses (down; 100%—CNV observed in all samples). While ( A ) and ( C ) display the summary data from 43 amelanotic melanomas (NCIT:C3802) and 10 254 ductal breast carcinom
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Lung adenocarcinoma cell line PC-9 SNVs. ( A ) Table of resulting variants ...
Published: 30 April 2024
Figure 4.
Lung adenocarcinoma cell line PC-9 SNVs. ( A ) Table of resulting variants for PC-9. ‘Digest’ shows the genomic location and the affected nucleotides of the variant, ‘Gene’—the affected gene, ‘Pathogenicity’—reported effect of the variant on human health, ‘Variant Effect’—effect of the variant on th
