Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.

Dermatofibrosarcoma protuberans (DFSP) is an aggressive spindle cell neoplasm. It is associated with the chromosomal translocation, t(17:22), which fuses the COL1A1 and PDGFbeta genes. We determined the characteristic gene expression profile of DFSP and characterized DNA copy number changes in DFSP by array-based comparative genomic hybridization (array CGH).

SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.

The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that brings together information from a broad range of resources, and provides it in manner particularly useful for genome-scale analyses. SOURCE's GeneReports include aliases, chromosomal location, functional descriptions, GeneOntology annotations, gene expression data, and links to external databases.

The Stanford Microarray Database: data access and quality assessment tools.

The Stanford Microarray Database (SMD; http://genome-www.stanford.edu/microarray/) serves as a microarray research database for Stanford investigators and their collaborators.

Integrating mutation data and structural analysis of the TP53 tumor-suppressor protein.

TP53 encodes p53, which is a nuclear phosphoprotein with cancer-inhibiting properties. In response to DNA damage, p53 is activated and mediates a set of antiproliferative responses including cell-cycle arrest and apoptosis. Mutations in the TP53 gene are associated with more than 50% of human cancers, and 90% of these affect p53-DNA interactions, resulting in a partial or complete loss of transactivation functions.

The Stanford Microarray Database.

The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two immediate goals for SMD are to serve as a storage site for microarray data from ongoing research at Stanford University, and to facilitate the public dissemination of that data once published, or released by the researcher. Of paramount importance is the connection of microarray data with the biological data that pertains to the DNA deposited on the microarray (genes, clones etc.

IARC p53 mutation database: a relational database to compile and analyze p53 mutations in human tumors and cell lines. International Agency for Research on Cancer.

The tumor suppressor p53 gene is the most frequently mutated gene in human cancer. To date, more than 10,000 mutations have been described in the literature, and these data are available in various electronic formats on the World Wide Web. Here we describe the structure and format of the different p53 datasets maintained and curated at the International Agency for Research on Cancer (IARC) in Lyon, France.

Sources of bias in the detection and reporting of p53 mutations in human cancer: analysis of the IARC p53 mutation database.

p53 gene encodes a transcription factor with tumor suppressive properties and to date, somatic mutation of this gene is the most common genetic event in human cancer. A relational database has been developed to facilitate the retrieval and analysis of these mutations at the International Agency for Research on Cancer (IARC) and it currently contains information on over 8000 individual tumors and cell lines. Many factors may influence the detection and reporting of mutations, including selection of tumor samples, study design, choice of methods, and quality control.

A specific spectrum of p53 mutations in lung cancer from smokers: review of mutations compiled in the IARC p53 database.

Mutations in the p53 gene are common in lung cancer. Using data from the the International Agency for Research on Cancer p53 mutation database (R1), we have analyzed the distribution and nature of p53 mutations in 876 lung tumors described in the literature. These analyses confirm that G to T transitions are the predominant type of p53 mutation in lung cancer from smokers.