Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome
Reactome describes biological pathways as chemical reactions that closely mirror the actual physical interactions that occur in the cell. Recent extensions of our data model accommodate the annotation of cancer and other disease processes. First, we have extended our class of protein modifications t...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2012-11-01
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| Series: | Cancers |
| Subjects: | |
| Online Access: | http://www.mdpi.com/2072-6694/4/4/1180 |
| _version_ | 1797701152976928768 |
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| author | Lincoln Stein Peter D'Eustachio Henning Hermjakob David Croft Guanming Wu Karen Rothfels Robin Haw Marija Milacic |
| author_facet | Lincoln Stein Peter D'Eustachio Henning Hermjakob David Croft Guanming Wu Karen Rothfels Robin Haw Marija Milacic |
| author_sort | Lincoln Stein |
| collection | DOAJ |
| description | Reactome describes biological pathways as chemical reactions that closely mirror the actual physical interactions that occur in the cell. Recent extensions of our data model accommodate the annotation of cancer and other disease processes. First, we have extended our class of protein modifications to accommodate annotation of changes in amino acid sequence and the formation of fusion proteins to describe the proteins involved in disease processes. Second, we have added a disease attribute to reaction, pathway, and physical entity classes that uses disease ontology terms. To support the graphical representation of “cancer” pathways, we have adapted our Pathway Browser to display disease variants and events in a way that allows comparison with the wild type pathway, and shows connections between perturbations in cancer and other biological pathways. The curation of pathways associated with cancer, coupled with our efforts to create other disease-specific pathways, will interoperate with our existing pathway and network analysis tools. Using the Epidermal Growth Factor Receptor (EGFR) signaling pathway as an example, we show how Reactome annotates and presents the altered biological behavior of EGFR variants due to their altered kinase and ligand-binding properties, and the mode of action and specificity of anti-cancer therapeutics. |
| first_indexed | 2024-03-12T04:32:14Z |
| format | Article |
| id | doaj.art-d6fd5ab8aa194249b0b9025361bf48ab |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-12T04:32:14Z |
| publishDate | 2012-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-d6fd5ab8aa194249b0b9025361bf48ab2023-09-03T10:04:13ZengMDPI AGCancers2072-66942012-11-01441180121110.3390/cancers4041180Annotating Cancer Variants and Anti-Cancer Therapeutics in ReactomeLincoln SteinPeter D'EustachioHenning HermjakobDavid CroftGuanming WuKaren RothfelsRobin HawMarija MilacicReactome describes biological pathways as chemical reactions that closely mirror the actual physical interactions that occur in the cell. Recent extensions of our data model accommodate the annotation of cancer and other disease processes. First, we have extended our class of protein modifications to accommodate annotation of changes in amino acid sequence and the formation of fusion proteins to describe the proteins involved in disease processes. Second, we have added a disease attribute to reaction, pathway, and physical entity classes that uses disease ontology terms. To support the graphical representation of “cancer” pathways, we have adapted our Pathway Browser to display disease variants and events in a way that allows comparison with the wild type pathway, and shows connections between perturbations in cancer and other biological pathways. The curation of pathways associated with cancer, coupled with our efforts to create other disease-specific pathways, will interoperate with our existing pathway and network analysis tools. Using the Epidermal Growth Factor Receptor (EGFR) signaling pathway as an example, we show how Reactome annotates and presents the altered biological behavior of EGFR variants due to their altered kinase and ligand-binding properties, and the mode of action and specificity of anti-cancer therapeutics.http://www.mdpi.com/2072-6694/4/4/1180pathway databasepathway visualizationnetwork visualizationcancer annotationEGFR signaling |
| spellingShingle | Lincoln Stein Peter D'Eustachio Henning Hermjakob David Croft Guanming Wu Karen Rothfels Robin Haw Marija Milacic Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome Cancers pathway database pathway visualization network visualization cancer annotation EGFR signaling |
| title | Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome |
| title_full | Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome |
| title_fullStr | Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome |
| title_full_unstemmed | Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome |
| title_short | Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome |
| title_sort | annotating cancer variants and anti cancer therapeutics in reactome |
| topic | pathway database pathway visualization network visualization cancer annotation EGFR signaling |
| url | http://www.mdpi.com/2072-6694/4/4/1180 |
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