Microarray Bioinformatic Tools

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 ACID]

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 Affymetrix NetAffx Analysis Center]

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

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 ArrayPipe]

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 ArrayProspector]

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 ArrayXPath]

Bayesian Analysis of Gene Expression Levels (BAGEL). This software has been used for numerous prominent studies, including two published in Science, and two published in PNAS. Jeffrey Townsend. - [Read more Bayesian Analysis of Gene Expression Levels (BAGEL)]

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 BEARR]

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 Bioconductor]

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 BioProspector]

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

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 Canadian Microarray Resources]

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 CARRIE]

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 CIBEX]

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 CompareProspector]

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 CONFAC]

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 Defining Transcriptional Programs in Vascular Endothelium]

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

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 Expression Profiler]

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 Gene Expression Data Analyzer]

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 GenMAPP]

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

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 GEPAS]

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 GFINDer]

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 GOAL]

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

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 GoSurfer]

Software for microarray image analysis. - [Read more GridGrinder]

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 KARMA]

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 MatchMiner]