Biomedical Engineering Reference
In-Depth Information
Table 8.3
(continued)
Name and
Reference
Descriptions and URL
HGMD [60]
The Human Gene Mutation Database (HGMD) is a database compiled at the Institute
of Medical Genetics, University of Wales School of Medicine, in the United Kingdom
(now merged into Cardiff University). HGMD started this effort more than 20 years .
ago, and as of 1996 the data became publicly available through the Internet. In recent
years the number of entries in the database has increased by about 5,000 per year. By
July 2005, the database contained 53,943 mutations in 2,081 genes and provides 1,877
reference cDNA sequences. Data in HGMD are collected through manual and comput-
erized scanning in hundreds of journals for articles describing germline mutations
causing human genetic disease.
URL: http://www.hgmd.org
IARC TP53
Database [61]
Most human cancers are accompanied by somatic mutation or abnormal expression of
the tumor suppressor gene TP53 (also called P53). Of the public databases on TP53
mutations developed so far, the TP53 Database by the International Agency for Research
on Cancer (IARC) is considered to be the most extensive. It compiles all TP53 gene
mutations identified in human cancers and cell lines that have been reported in the
peer-reviewed literature since 1989. The R10 release (July 2005) contains 21,587
somatic mutations, 283 germline mutations and functional data on 426 mutant proteins.
URL: http://www-p53.iarc.fr/index.html
ONCOMINE [62]
Featured in the
Journal of the American Medical Association
and Science Netwatch,
ONCOMINE is a cancer microarray database with a web-based data-mining platform
aimed at facilitating discovery from genome-wide expression analyses. The database
was developed at University of Michigan. By midyear 2005, it contained 90 gene
expression data sets comprising 71 million gene expression measurements from more
than 6,300 microarray experiments. Differential expression analyses comparing most
major types of cancer with respective normal tissues as well as a variety of cancer sub-
types and clinical-based and pathology-based analyses are available for exploration.
Data can be queried and visualized for a selected gene across all analyses or for multiple
genes in a selected analysis. Furthermore, gene sets can be limited to clinically important
annotations including secreted, kinase, membrane, and known gene-drug target pairs to
facilitate the discovery of novel biomarkers and therapeutic targets.
URL: http://141.214.6.50/oncomine/main/index.jsp
Stanford Microarray
Database [63]
The Stanford Microarray Database (SMD) is a research tool for hundreds of Stanford
researchers and their collaborators. In addition, it serves as a resource for the entire bio-
logical research community by providing unrestricted access to microarray data pub-
lished by SMD users and by disseminating its source code.
URL: http://genome-www5.stanford.edu
T1Dbase [64]
T1DBase is a public website and database that supports type 1 diabetes (T1D) research.
As a joint development effort between the Institute for Systems Biology, Juvenile Diabe-
tes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, and
the Juvenile Diabetes Research Foundation International, it is currently focused on the
molecular genetics and biology of T1D susceptibility and pathogenesis. The database
collects information across human, rat, and mouse species from public sources and
from collaborating laboratories. The current data scope includes annotated genomic
sequences for suspected T1D susceptibility regions; microarray data; functional annota-
tion of genes active in beta cells; and “global” data sets, generally from the literature,
that are useful for systems biology studies. The data are integrated and presented in a
form that is useful for T1D researchers. Software tools for analyzing the data are also
available. All data are open access and all software is open source.
URL: http://t1dbase.org
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