My Microarray Software Comparison - Public Microarray Database and Gene Expression Database

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Definition of public microarray database
Suggested readings
   Database and sharing
   Standardization
Public microarray database (in alphabetical order)

[ ArrayExpress | ChipDB| ExpressDB | Gene Expression Atlas | Gene Expression Database (GXD) | Gene Expression Omnibus | GeneX | GermOnline | Human Gene Expression Index (HuGE Index) | List Of Lists Annotated (LOLA) | M-CHiPS (Multi-Conditional Hybridization Intensity Processing System) | MUSC DNA Microarray Database | NASCArrays | Oncomine | Public Expression Profiling Resource (PEPR) | READ (RIKEN cDNA Expression Array Database) | Rice Expression Database (RED) | RNA Abundance Database (RAD) | Saccharomyces Genome Database (SGD): Expression Connection | SGMD | Standford Microarray Database (SMD) | Yale Microarray Database | yeast Microarray Global Viewer (yMGV) ]

Gene expression database (in alphabetical order)

[ 3D-GeneExpression Database| BODYMAP | Gene Resource Locator | RNA Abundance Database (RAD) | TissueInfo ]

Definition of public microarray database and gene expression database

Suggested readings

1. Anderle P, Duval M, Draghici S, Kuklin A, Littlejohn TG, Medrano JF, Vilanova D, Roberts MA. Gene expression databases and data mining.
   Biotechniques. 2003 Mar;Suppl:36-44. [PubMed]
2. Sherlock G, Ball CA. Microarray databases: storage and retrieval of microarray data. Methods Mol Biol. 2003;224:235-48. [PubMed]
3. Miles MF. Microarrays: lost in a storm of data? Nat Rev Neurosci. 2001 Jun;2(6):441-3. [PubMed]
4. Becker KG. The sharing of cDNA microarray data. Nat Rev Neurosci. 2001 Jun;2(6):438-40. [PubMed]
5. Geschwind DH. Sharing gene expression data: an array of options. Nat Rev Neurosci. 2001 Jun;2(6):435-8. [PubMed]
6. Gardiner-Garden M, Littlejohn TG. A comparison of microarray databases. Brief Bioinform. 2001 May;2(2):143-58. [PubMed]

1. Stoeckert CJ, Causton HC, Ball CA. Microarray databases: standards and ontologies. Nat Genet. 2002 Dec;32 Suppl 2:469-73. [PubMed]
2. Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 2002 Aug 23;3(9):RESEARCH0046.  [PubMed][pdf]
3. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001 Dec;29(4):365-71. [PubMed]
   

Public microarray database (in alphabetical order)

• ArrayExpress - A public repository for microarray based gene expression data maintained by European Bioinformatics Institute.
• ChipDB - A searchable database of gene expression
• ExpressDB - A relational database containing yeast and E. coli RNA expression data. Reference[PubMed]
• Gene Expression Atlas - A database for gene expression profile from 91 normal human and mouse samples across a diverse array of tissues, organs, and cell lines. Reference[PubMed][pdf]
• Gene Expression Database (GXD) - A database of Mouse Genome Informatics at the Jackson laboratory.
• Gene Expression Omnibus - A database in NCBI for supporting the public use and disseminating of gene expression data. Reference[PubMed]
• GeneX -  National Center for Genome Resources's initative to provide an Internet-available repository of gene expression data
• GermOnline - GermOnline provides information and microarray expression data for genes involved in mitosis and meiosis, gamete formation and germ line development across species. Reference[PubMed]
• Human Gene Expression Index (HuGE Index) -  aims to provide a comprehensive database to understand the expression of human genes in normal human tissues. Reference[PubMed]
• List Of Lists Annotated (LOLA) - a web driven database allowing researchers to identify and correlate significant subsets of genes derived from microarray expression profiling.
• M-CHiPS (Multi-Conditional Hybridization Intensity Processing System) - M-CHIPS is a data warehousing concept and focuses on providing a structure suitable for statistical analysis of a  microarray database's entire components including the experiment annotations. Reference [PubMed][web supplement]
• MUSC DNA Microarray Database - MUSC DNA Microarray Database is a web-accessible archive of DNA microarray data. Reference[PubMed]
• NASCArrays - a repository for Affymetrix data generated by NASC's transcriptomics service. Reference[PubMed]
• Oncomine - The goal of this project is to curate publicly available cancer microarray studies and provide data mining tools to efficiently query genes and datasets of interest as well as meta-analyze groups of studies. Links to various bioinformatics resources have been implemented including Unigene, Swissprot, Biocarta, HPRD, and KEGG, among others.
  
• Public Expression Profiling Resource (PEPR) - A web oracle data warehouse of quality control and standard operating procedure (QC/SOP) Affymetrix data. Reference[PubMed]
• READ (RIKEN cDNA Expression Array Database)- A database maintained by RIKEN (The institute of Physical and Chemical Research), Japan. Reference[PubMed]
• Rice Expression Database (RED) - RED holds raw and normalized data from expression profiles obtained by the Rice Microarray Project and other research groups. These data are open to the public less than one year after sending the data to each research group.
  
• RNA Abundance Database (RAD) - RNA Abundance Database (RAD) is a public gene expression database designed to hold data from array-based and nonarray-based (SAGE) experiments. The ultimate goal is to allow comparative analysis of experiments performed by different laboratories using different platforms and investigating different biological systems.
• Saccharomyces Genome Database (SGD): Expression Connection -  A gene expression database of Saccharomyces genome database in Stanford University, provide simultaneous search of several microarray studies result for gene expression data for a given gene or ORF. Reference[PubMed]
• Soybean Genomics and Microarray Database (SGMD) - The 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. Reference[PubMed]
• Standford Microarray Database (SMD) - Standford Microarray Database (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. Data is released to the public at the researcher's discretion or upon publication. Reference[PubMed]
• Yale Microarray Database
• yeast Microarray Global Viewer (yMGV) - A database for yeast gene expression data maintained by Laboratoire de genetique moleculaire, Ecole Normale Superieure. Reference 1[PubMed]; Reference 2[PubMed]; Reference 3[PubMed]
  

Gene expression database (in alphabetical order)

• 3D-GeneExpression Database - Preliminary structure for a database of 3D-visualization of developmental gene expression
• BODYMAP - A databank of gene expression information of human and mouse genes, created by random sequencing of clones in 3'-directed cDNA libraries
• Gene Resource Locator - the goal is to map millions of ESTs to the human genome for the study of the exon-intron structures of genes, the alternative splicing of pre-mRNAs, the promoter regions of full-length-enriched cDNA sequences, and the gene-expression patterns associated with ESTs.
• RNA Abundance Database (RAD)  - RNA Abundance Database (RAD) is a public gene expression database designed to hold data from array-based and nonarray-based (SAGE) experiments. The ultimate goal is to allow comparative analysis of experiments performed by different laboratories using different platforms and investigating different biological systems.
• TissueInfo - an online database determines the tissue expression profile of a sequence by comparing the given sequence against the EST database. Each EST comes from a library derived from a specific tissue type