A global evaluation of microarray dedicated databases. PDF. Sophie Lemoine. - [Read more]

The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ont - [Read more]

Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required. - [Read more]

Public repository for microarray based gene expression data; contains several curated gene expression datasets. - [Read more]

ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of repor - [Read more]

ArrayProspector is a set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for links between two genes. - [Read more]

ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams. - [Read more]

BASE - BioArray Software Environment. BASE a free web-based database solution for the massive data generated by microarray analysis. Released under GNU General Public License. - [Read more]

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in bot - [Read more]

BiNGO is a Java-based tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. - [Read more]

Bioconductor is an open source and open development software project that aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data. - [Read more]

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations. - [Read more]

The MGuide (version 2.0). The Brown Labs complete guide to microarraying for the molecular biologist. - [Read more]

Contact information, availabilities and expertise of Canadian microarray centres; includes labs that supply cDNA or oligonucleotide spotted arrays and other services, and labs that can analyse RNA with Affymetrix chips. - [Read more]

Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely invol - [Read more]

The Center for Information Biology gene EXpression database (CIBEX) is a public repository for gene expression experimental data. The database system is compliant with the MIAME standard. - [Read more]

A program for calculating cluster enrichment analysis and integrated visualization of expression, annotation and transcription factor binding site data using the Gene Ontology. - [Read more]

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species. - [Read more]

The Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from t - [Read more]

Database for Annotation, Visualization and Integrated Discovery (DAVID) is a web-based tool that provides integrated solutions for the annotation and analysis of genome-scale datasets derived from high-throughput technologies such as microarray and proteo - [Read more]

This website contains microarray analysis software (Argus and Z-pool), an Endothelial Cell Expression Database, and other resources related to Vascular Endothelium research. See the PubMed abstracts for more information. - [Read more]

Doelan is an tool designed to monitor the quality of DNA microarray production. - [Read more]

Useful for summarizing the predominant biological "theme" of a given gene list. From a list of genes from microarray or other genome-scale experiments, EASE can rapidly calculate over-representation statistics for every possible Gene Ontology term with re - [Read more]

ermineJ is a tool for the analysis of gene sets (user defined or those defined by GO terms) in expression data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who - [Read more]

ExpressDB - a relational database containing yeast and E. coli RNA expression data. - [Read more]

Expression Profiler is a web based platform for microarray data analysis developed at the EBI. This resource is integrated with the ArrayExpress database, a public repository for microarray data. - [Read more]

The Gene Expression Data Analyzer (GEDA) is a tool for discovering differential gene expression in a subset of patients. It is tailored to cancer-related microarray studies and offers extensive options for visualization, classification and normalization. - [Read more]

GeneX-Lite - a client software application providing an interface to relational database managment systems (RDBMS). The application interface allows the user to load, manage, analyze, visualize and query gene expression data. RDBMS provides storage of the data and analysis/visualization results. Free download. NCGR.org - [Read more]

GenMAPP (Gene MicroArray Pathway Profiler) is a microarray expression data visualization tool, allowing data to be viewed on maps representing gene groupings and biological pathways. - [Read more]

Gene Expression Omnibus: - GEO is a gene expression/molecular abundance repository supporting MIAME compliant data submissions, and a curated, online resource for gene expression data browsing, query and retrieval. NCBI - [Read more]

Gene expression and hybridization array data repository; online resource for retrieval of gene expression data from any organism or artificial source. - [Read more]

The Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data including data pre-processing, clustering, sample comparison, data mining based on GO terms (FatiGO), and annnotation. Also included are tools - [Read more]

Genome Functional INtegrated Discoverer (GFINDer) takes a list of gene/clone IDs with classification information as input, and allows the user to characterize the different gene classes in the list using annotations of various types from several different - [Read more]

Gene Ontology Automated Lexicon (GOAL) is a tool for the functional analysis of data from SAGE and microarray experiments. Gene Ontology terms are used as the basis for statistical analysis. - [Read more]

GoMiner organizes and allows the visualization of large sets of genes based on Gene Ontology classifications. - [Read more]

GoSurfer is a tool for visualizing and comparing gene sets by mapping them onto Gene Ontology (GO) information in the form of a hierarchical tree. It is useful for investigating the results of microarray analyses or genome-wide computations. - [Read more]

Software for microarray image analysis. - [Read more]

HuGEIndex Database. - [Read more]

KARMA (Keck Array Manager and Annotator) allows you compare and annotate your own microarrays against other available arrays. Comparison of arrays can be achieved within the same species as well as across species (array comparison is based on UniGene Clu - [Read more]

Multi-Conditional Hybridization Intensity Processing System. A data warehousing concept that focuses on providing a structure for the statistical analysis of the entire components of microarray database's including the experimental annotations. - [Read more]

MatchMiner is a tool to compare and convert gene identifiers. Users can translate single or lists of identifiers from one form to another, or compare two lists of identifiers for common gene references. - [Read more]

maxd - a data warehouse and visualisation environment for genomic expression data. maxdLoad2, maxdView. - [Read more]

Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites. - [Read more]

MedMiner can be used to select genes from a microarray set based on GeneCards information. Based on the genes selected one can then search PubMed abstracts using known gene synonyms and other user-specified search parameters. The PubMed search can also - [Read more]

MIAME (minimum information about a microarray experiment) compliant microarray data submission tool. - [Read more]

Group facilitating the development of an international repository for gene expression data and the experimental and database standards required for such an endeavour. - [Read more]

MicroArray Project System (MAPS). MAPS is a MicroArray Project System for the management and interpretation of microarray gene expression experiment data. NIEHS - Microarray Group - [Read more]

Protocols, analysis and resources; BLAST against the 15K set cDNA library clones (from 15,000 human UniGene clusters; clones are available). - [Read more]

NOMAD. An open source system of software for storing and querying the results of microarray experiment data. UCSF Nomad - [Read more]

Oligodb generates oligos suitable for expression experiments based on predicted gene transcripts from the Ensembl project. One can search for transcripts via keyword, or do a batch search by providing a list of Ensembl identifiers. - [Read more]

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Functional groupings of lists of differentially expressed genes can be created using Onto-Express. Contains tools for assessing the functional bias for sets of - [Read more]

An XML-based Java application is described that provides a function-oriented overview of the results of cluster analysis of gene-expression microarray data based on Gene Ontology terms and associations. The application generates one HTML page with listi - [Read more]

A server for the detection, comparison and verification of transcription factor binding site motifs in promoters. POBO bootstrap analysis applied to one or two clusters of co-regulated genes detects motifs under extreme levels of representation. - [Read more]

Using current releases of genomic sequence data, ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and ProbeLynx reports specificity in - [Read more]

RAB - RNA Abundance Database - [Read more]

Bono, H., Kasukawa, T., Hayashizaki, Y., and Okazaki, Y. READ: RIKEN Expression Array Database Nucleic Acids Research, 30, 211-213 (2002). - [Read more]

ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program. This knowledge environment includes freely available data derived from small molecules and small-molecule screens. ChemBank is intended to guide chemists synthesizing novel compounds or libraries, to assist biologists searching for small molecules that perturb specific biological pathways, and to catalyze the process by which drug hunters discover new and effective medicines. - [Read more]

Tool for cross-referencing microarray data derived from different species and across different expression analysis platforms. Built using the analysis of ESTs, the TIGR Gene Index (TGI), and Eukaryotic Gene Orthologs (EGO) databases. - [Read more]

Eisen Lab software for microarry image processing, analysis and visualization; available for download to windows platforms only; free with registration for non-commercial use. - [Read more]

Stanford Online Universal Resource for Clones and ESTs pools publicly available data commonly sought for any clone, GenBank accession, or gene from human, mouse, rat. - [Read more]

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. - [Read more]

A list of open-source software packages available for free from The Institute for Genomic Research (TIGR). - [Read more]