title: MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways.
abstract: Despite on-going research, metastatic melanoma survival rates remain low and treatment options are limited. Researchers can now access a rapidly growing amount of molecular and clinical information about melanoma. This information is becoming difficult to assemble and interpret due to its dispersed nature, yet as it grows it becomes increasingly valuable for understanding melanoma. Integration of this information into a comprehensive resource to aid rational experimental design and patient stratification is needed. As an initial step in this direction, we have assembled a web-accessible melanoma database, MelanomaDB, which incorporates clinical and molecular data from publically available sources, which will be regularly updated as new information becomes available. This database allows complex links to be drawn between many different aspects of melanoma biology: genetic changes (e.g., mutations) in individual melanomas revealed by DNA sequencing, associations between gene expression and patient survival, data concerning drug targets, biomarkers, druggability, and clinical trials, as well as our own statistical analysis of relationships between molecular pathways and clinical parameters that have been produced using these data sets. The database is freely available at http://genesetdb.auckland.ac.nz/melanomadb/about.html. A subset of the information in the database can also be accessed through a freely available web application in the Illumina genomic cloud computing platform BaseSpace at http://www.biomatters.com/apps/melanoma-profiler-for-research. The MelanomaDB database illustrates dysregulation of specific signaling pathways across 310 exome-sequenced melanomas and in individual tumors and identifies the distribution of somatic variants in melanoma. We suggest that MelanomaDB can provide a context in which to interpret the tumor molecular profiles of individual melanoma patients relative to biological information and available drug therapies.
authors.affiliation: Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland , Auckland , New Zealand.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Trevarton
authors.forename: Michael B
authors.initials: MB
authors.lastname: Mann
authors.forename: Christoph
authors.initials: C
authors.lastname: Knapp
authors.forename: Hiromitsu
authors.initials: H
authors.lastname: Araki
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Wren
authors.forename: Steven
authors.initials: S
authors.lastname: Stones-Havas
authors.forename: Michael A
authors.initials: MA
authors.lastname: Black
authors.forename: Cristin G
authors.initials: CG
authors.lastname: Print
keywords: BaseSpace; MelanomaDB; gene set analysis; melanoma; molecular pathway; mutation