Gene Expression Database

Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L et al. A gene expression database for the molecular biology of cancer. Nat Genet 2000 24 236-44. 

Scherf, U. and Ross, D.T., A gene expression database for the molecular pharmacology of cancer, Nat. Genet., 24, 236-244, 2000. 

Fig. 1. Whole scheme of gene module search from gene expression database. The system consists of four steps (a) discretization of query and dafabase, (b) database masking, (c) enumeration of core modules, and (d) module merging. In fhis example, the query and the database are discretized into only three degrees ffigh (+f)," Low (-1), and Other expressions (0)".

Public repositories of microarray gene expression data have been developed to store the results of array experiments ArrayExpress (32) in Europe, Gene Expression Omnibus (GEO) in the United States (33), and the Center for Information Biology Gene Expression Database (CIBEX) (34) in Japan. Many journals already require an accession number (indicating that a data set has been submitted to one of these public databases) prior to publication. 

CIBEX Center for Iirformation Biology Gene Expression Database cibex.nig.ac.jp... 

Ikeo K, Ishi-i J, Tamura T et al. CIBEX center for information biology gene expression database. CRBiol 2003 326 1079-1082. 

This set of estrogen-regulated genes were then used to classify both breast cancer cell lines and specimens, whose expression data were publicly available in on-line databases (the NCI60 gene expression database for the molecular... 

Hurtt ME, Streck RD, Kumpf SW, et al. Fetal map A gene expression database for predicting potential involvement in developmental toxicity for all druggable genes. Birth Defects Res PtA. 2007 29 352. 

MENT http //mgrc. kribb. re. kr 8080/MENT/ DNA methylation and gene expression database of cancers... 

In this paper we describe the basic design of a microarray gene expression database to help microarray users and their informatics teams set up their information services. The first version of the microarray database object model ArrayExpress, which is described here, was developed at the European Bioinformatics Institute (EBI) in collaboration with the German Cancer Research Centre (DKFZ) and posted on the Internet in November, 1999 (see (http //www.ebi.ac.uk/arrayexpress)). A relational database implementation maxd based on the ArrayExpress object model was conducted at the University of Manchester (http //bioinf.man.ac.uk/microarray/resources.html) and is widely used for microarray laboratory informatics support. 

The data model is able to capture detailed experiment annotation. Aimotating the experiments in such detail may be regarded as an unnecessary burden by some laboratories. In the current gene expression databases, some of the samples are armotated rather briefly, for instance as control . Laboratories should consider the tradeoffs of investing resources in annotation of their experiments in more or less detail, and being able to use the obtained data at a later date. 

Gene expression databases can be made from two sources, ESTs (Expressed Sequence Tags) or DNA chip expression data. 

There are currently no publicly available DNA chip expression databases, however the Microarray Gene Expression Database Group (MGED) [3] at the EBI aims to facilitate the creation of a gene expression data repository. 

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