Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome

Cancers

Marija Milacic²  Robin Haw²  Karen Rothfels²  Guanming Wu²  David Croft¹  Henning Hermjakob¹  Peter D𠆞ustachio³ 

[1] European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; E-Mails:;Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON, M5G0A3, Canada; E-Mails:;Department of Biochemistry, NYU School of Medicine, New York, NY 10016, USA; E-Mail:

关键词: pathway database;    pathway visualization;    network visualization;    cancer annotation;    EGFR signaling;   

DOI  :  10.3390/cancers4041180

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2012 by the authors; licensee MDPI, Basel, Switzerland.