Microarray databases
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[edit] Microarray databases - Quick Links
[edit] Microarray databases - Web Resources
Gene Expression Omnibus
GEO. GEO is a gene expression and hybridization array data repository, as well as an online resource for the retrieval of gene expression data from any organism or artificial source.
ArrayExpress Database
Public repository for microarray based gene expression data. ArrayExpress is a public repository for microarray data, which is aimed at storing well annotated data in accordance with MGED recommendations
TranscriptomeBrowser
TranscriptomeBrowser (TBrowser) host a large database of transcriptional signatures extracted from GEO public microarray repository. TS have been produced using a new algorithm called "Density Based Filtering And Markov Clustering" (DBF-MCL). The purpose of DBF-MCL is to extract informative genes in a given dataset and to classify them into homogeneous clusters. The current database contains about 20,000 TS derived from ~ 1,500 microarray datasets (~222 millions expression values). Each TS was tested for functional enrichment using annotation obtained from numerous ontologies or curated databases (Gene Ontology, KEGG, BioCarta, Swiss-Prot, BBID, SMART, NIH Genetic Association DB, COG/KOG...) using the DAVID knowledgebase. TBrowser comes with a sophisticated search engine so that users can perform combined queries using boolean operators. TBrowser functionalities can be extend using plug in development (Java).
GENEVESTIGATOR
A popular multi-organism gene expression database and online analysis tool. Users can look at how genes of interest are expressed in many different tissues, developmental stages, stimuli/diseases/drugs, and mutations. These summarized profiles are compiled from thousands of Affymetrix microarrays (as of May 2007: >10'000 arrays from mouse, rat and arabidopsis). Tools for biomarker search, clustering and pathway analysis are also available. The tool was developed at and is provided by the Swiss Federal Institute of Technology in Zurich.
RNA Abundance Database
RAD (RNA Abundance Database) is a public gene expression database designed to hold data from array-based (microarrays, high-density oligo arrays, macroarrays) and nonarray-based (SAGE) experiments. The ultimate goal is to allow comparative analysis of exp
RAD :: RNA Abundance Database
RNA Abundance Database.
Microarray expression data
Saccharomyces Genome Database - Expression Connection allows you to search gene expression data from multiple microarray studies.
ExpressDB
Relational database for yeast RNA expression data. ExpressDB is a relational database for maintaining yeast RNA expression data. It is intended as a demonstration of how such data can be managed, and of the benefits such management confers. As of July, 1999, over 17.5 million pieces of information have been loaded into ExpressDB deriving from 11 source studies. The EXD web query system allows data from multiple source studies to be retrieved to user specifications and collated by ORF name.
Yeast Microarray Global Viewer
A yeast microarray data mining tool for genome-wide yeast expression data. Database includes much of the available expression data published on yeast microarrays.
yMGV. The yeast Microarray Global Viewer was created 3 years ago as a database that houses a collection of Saccharomyces cerevisiae and Schizosaccharo myces pombe microarray data sets published in 82 different articles. yMGV couples data mining tools with a user-friendly web interface so that, with a few mouse clicks, one can identify the conditions that affect the expression of a gene or list of genes regulated in a set of experiments. One of the major new features we present here is a set of tools that allows for inter-organism comparisons. This should enable the fission yeast community to take advantage of the large amount of available information on budding yeast transcriptome.
SMD : Stanford Microarray Database
Stores raw and normalized data from microarray experiments, as well as their corresponding image files. SMD provides interfaces for data retrieval, analysis and visualization.
SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization.
Bodymap
A databank of gene expression information of human and mouse genes, created by random sequencing of clones in 3'-directed cDNA libraries.
Data bank of expression information of human and mouse genes, novel or known, in various tissues or cell types and various timings. The first generation map was created by random sequencing. BodyMap is a human and mouse gene expression database that has been maintained since 1993. It is based on site-directed 3ยน-ESTs collected from non-biased cDNA libraries constructed at Osaka University and contains more than 270, 000 sequences from 60 human and 38 mouse tissues. The site-directed nature of the sequence tags allows unequivocal grouping of tags representing the same transcript and provides abundance information for each transcript in different parts of the body. Our collection of ESTs was compared periodically with other public databases for cross referencing. The histological resolution of source tissues and unique cloning strategy that minimized cloning bias enabled BodyMap to support three unique mRNA based experiments in silico. First, the recurrence information for clones in each library provides a rough estimate of the mRNA composition of each source tissue. Second, a user can search the entire data set with nuleotide sequences or keywords to assess expression patterns of particular genes. Third, and most important, BodyMap allows a user to select genes that have a desired expression pattern in humans and mice.
HugeIndex
mRNA expression levels of human genes in normal tissues. Human Gene Expression (HuGE) Index database was established to serve as a public repository for gene expression data on normal human tissues using high-density oligonucleotide arrays. This resource currently contains the results of 59 gene expression experiments on 19 human tissues. We provide interactive tools for researchers to query and visualize our data over the Internet.
The Mouse SAGE Site
Database of public mouse SAGE libraries. The Mouse SAGE Site is a web-based database of all available public libraries generated by the Serial Analysis of Gene Expression (SAGE) from various mouse tissues and cell lines. The database contains mouse SAGE libraries organized in a uniform way and provides web-based tools for browsing, comparing and searching SAGE data with reliable tag-to-gene identification. A modified approach based on the SAGEmap database is used for reliable tag identification.
The PEPR GeneChip data warehouse
Implementation of a dynamic time series query tool (SGQT) with graphical interface. We have designed and implemented a public resource of expression profile data containing 1024 human, mouse and rat Affymetrix GeneChip expression profiles, generated in the same laboratory, and subject to the same quality and procedural controls (Public Expression Profiling Resource PEPR). Our Oracle-based PEPR data warehouse includes a novel time series query analysis tool (SGQT), enabling dynamic generation of graphs and spreadsheets showing the action of any transcript of interest over time. In this report, we demonstrate the utility of this tool using a 27 time point, in vivo muscle regeneration series. This data warehouse and associated analysis tools provides access to multidimensional microarray data through web-based interfaces, both for download of all types of raw data for independent analysis, and also for straightforward gene-based queries.
GenePaint.org
An atlas of gene expression patterns in the mouse embryo. High-throughput instruments were recently developed to determine gene expression patterns on tissue sections by RNA in situ hybridization. The resulting images of gene expression patterns, chiefly of E14.5 mouse embryos, are accessible to the public. This relational database is searchable for gene identifiers and RNA probe sequences. Moreover, patterns and intensity of expression in 100 different embryonic tissues are annotated and can be searched using a standardized catalog of anatomical structures. A virtual microscope tool, the Zoom Image Server, was implemented in GenePaint.org and permits interactive zooming and panning across about 15,000 high-resolution images.
NASCArrays
A repository for microarray data generated by NASCs transcriptomics service. NASC operates an Affymetrix GeneChip (microarray) service for the Arabidopsis thaliana community. The data are accessible through text searching and a series of data mining tools. All data are annotated with sample preparation details, and the original Affymetrix data are available for download. The database aims to be MIAME supportive and provide a coordinated resource for re searchers interested in the transcriptome of Arabidopsis.
Yeast Diauxic Shift
Complete yeast genome expression over diauxic shift. Exploring the metabolic and genetic control of gene expression on a genomic scale.
SGMD :: Soybean Genomics and Microarray Database
Sequence repository for ESTs and MIAME microarray experiment database. Allows exploration of expression levels of database's EST clones and correlation of expression levels with function.
SGMD. The Soybean Genomics and Microarray Database (SGMD) attempts to provide an integrated view of the interaction of soybean with the soybean cyst nematode and contains genomic, EST and microarray data with embedded analytical tools allowing correlation of soybean ESTs with their gene expression profiles. SGMD provides analytical tools to mine the microarray data quickly by integrating many analysis methods within the database itself. The expression profiles of genes at time intervals during the first 8 days of nematode invasion is searchable by gene name or GenBank accession number. Recent developments include the addition of a searchable database for soybean cyst nematode ESTs and photographs of the invasion process at time points examined using microarrays.
Interferon Stimulated Gene Database
Genes induced by treatment with interferons. Interferons (IFN) are a family of multifunctional cytokines that activate transcription of a subset of genes. The gene products induced by IFN are responsible for the antiviral, antiproliferative and immunomodulatory properties of this cytokine. In order to obtain a more comprehensive understanding of the genes regulated by IFNs we have used different microarray formats to identify over 400 interferon stimulated genes (ISG). To facilitate the dissemination of this data we have compiled a database comprising the ISGs assigned into functional categories. The database is fully searchable and contains links to sequence and Unigene information.
MEPD
Gene expression data from the small freshwater fish Medaka (Oryzias latipes). The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by images and by descriptions through parameters such as staining intensity, category and comments and through a comprehensive, hierarchically organized dictionary of anatomical terms. Sequences of the ESTs are available and searchable through BLAST. ESTs in the database are clustered upon entry and have been blasted against public data-bases. The BLAST results are updated regularly, stored within the database and searchable. The MEPD is a project within the Medaka Genome Initiative (MGI) and entries will be interconnected to integrated genomic map databases.
MAGEST
Ascidian (Halocynthia roretzi) gene expression patterns. MAGEST is a database of maternal gene expression information for an Ascidian, Halocynthia roretzi. The ascidian has become an animal model in developmental biological research because it shows the simple developmental process and belongs to the one of chordate groups. We register some kinds of dataset with the MAGEST database, e.g., the 3-prime and 5-prime tag sequences from the fertilized egg cDNA library, the result of similarity search against the GenBank and the expression data from whole mount in situ hybridization. For the last two years, the data retrieval systems have been improved in several points and the tag sequence entries have increased to over 20,000 clones. Beside these data, we try to produce the amino acid fragment sequences predicted from the EST data set. Using these data from comprehensive view, we will get some new information of the gene functions.
GNF SymAtlas (supercedes Gene Expression Atlas)
Version 2 dataset of Gene Expression Atlas - a database for gene expression profile with >30,000 human and mouse targets
Gene Expression Atlas: Text Query
A database for gene expression profile from 91 normal human and mouse samples across a diverse array of tissues, organs, and cell lines.
ChipDB
ChipDB - A searchable database of gene expression.
Yale Microarray Database (YMD)
Collaborative effort between several labs to meet the need to archive and retrieve via query statements microarray images and analysis data from many different investigators.
DRAGON Database
Database referencing of array genes online. Tools to search, annotate and list significantly regulated genes (SNOMAD), visualize data, or view a map of the human transcriptome.
GermOnline Systems Browser
GermOnline provides information and microarray expression data for genes involved in mitosis and meiosis, gamete formation and germ line development across species.
RED :: Rice Expression Database
RED holds raw and normalized data from expression profiles obtained by the Rice Microarray Project. These data are open to the public less than one year after sending the data to each research group.
Another MicroArray Database. AMAD
AMAD is a flat file, web driven database system written entirely in PERL and javascript, and intended for use with microarray generated data.
The Gene Expression Database (GXD) - About GXD
The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data, making these data freely available in formats appropriate for analysis.
READ: Riken Expression Array Database
Database of expression profile data from the RIKEN mouse cDNA microarray. Stores the microarray experimental data and information, and provides web interfaces to retrieve, analyze and display data.
ExpressDB from Harvard
A relational database containing yeast and E. coli RNA expression data. Contains more than 20 million pieces of information loaded from numerous published and in-house expression studies.
South Carolina DNA Microarray Project Management System and the MUSC DNA Microarray Database
The MUSC DNA Microarray Database was developed using uArrayDB, a web-based relational database system for archiving and exchanging DNA microarray data.
SOURCE Search
SOURCE is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, ...
GeneNote is a database of human genes from Weizmann Institute of Science
GeneNote is a database of human genes and their expression profiles in healthy tissues, based on Weizmann Institute array experiments performed on Affymetrix HG-U95 set A-E.
ExpressDB
ExpressDB Information Page. ExpressDB was originally a relational database containing yeast and E. coli RNA expression data. In 2000 it contained more than 20 million pieces of information from numerous published and in house studies. The server is now decommisioned but you can still download the datasets.
Human Genome Expression Index (HuGE Index)
Human Gene Expression (HuGE) Index database to serve as a public repository for gene expression data on normal human tissues using high-density oligonucleotide arrays.
5 prime sage search
5'-end SAGE for the analysis of transcriptional start sites
The Genomic Service from the ENS Biology Department (SGDB)
A global evaluation of microarray dedicated databases.Compared among 23 databases, 4 where evaluated more precisely (BASE, GeneTraffic, MaxD, RAD ). Gives suggestions for an efficient in-house database warehousing.
NCGR :: GeneX-Lite :: Gene Expression Lite
Client application that provides an interface to a persistent storage RDBMS. The client application interface allows the user to load, manage, analyze, visualize and query gene expression data.
PLEXdb (Plant Expression Database)
Gene expression data for plants and plant pathogens. PLEXdb serves as a bridge to integrate new and rapidly expanding gene expression profile data sets with traditional structural genomics and phenotypic data.
