1 | Signature Evaluation Tool (SET) http://microarray.ym.edu.tw:8080/tools/module/set/index.jsp?mode=home | Java-based tool (using Golub's weighted voting algorithm) for incorporating the visual presentation of prediction strength for each array sample. |
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2 | Arabidopsis Co-Expression Tool (ACT) http://www.arabidopsis.leeds.ac.uk/ACT/ | Web-based tool and database for plant gene analysis derived from Arabidopsis thaliana microarray data set obtained from the Nottingham Arabidopsis Stock Centre. |
| | URL not working as on May 16, 2015 URL not working as on May 16, 2015 |
3 | SOURCE http://source-search.princeton.edu/ | Contains information from a broad range of resources, which are useful for genome-scale analyses. |
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4 | DEEP - Differential Expression Effector Prediction http://deep.bioinf.med.uni-goettingen.de/ | Implemented in the Java programming language and consists of three parts: the DEEP core server, a JSP-based web interface and a downloadable Java client. |
| | URL not working as on May 16, 2015 URL not working as on May 16, 2015 |
5 | Expression Data http://expressiondata.org/ex/ | Provides high quality and robust datasets representing gene expression across tissue types, stages of development and experimental conditions. |
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6 | ROAD - Rice Oligonucleotide Array Database http://www.ricearray.org/ | Database of rice microarray hybridizations and visualization tools for extraction of geneA0expressionA0profiles using gene and microarray element identifications. It also supports meta-analysis of genes expressed in different tissues and at developmental stages. |
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7 | TEAM- Tool for the integration of Expression http://humgen.med.uu.nl/~lude/team | Tools and database for analysis and reporting functionality and a graphical viewer that is able to view genetic linkage, association, and expression data simultaneously. |
| | URL not working as on May 16, 2015 URL not working as on May 16, 2015 |
8 | GATE- Grid Analysis of Time series Expression http://amp.pharm.mssm.edu/maayan-lab/gate.htm | An integrated computationalA0softwareA0platform for the analysis and visualization of high-dimensional biomolecular time series. |
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9 | DRASTIC - Database Resource for the Analysis of Signal Transduction In Cells http://www.drastic.org.uk/ | Relational database of plant expressed sequence tags and genes up-or-down-regulated in response to various pathogens, chemical exposure or other treatments such as drought, salt and low temperature. |
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10 | SAM- Shoot Apical Meristem http://sam.truman.edu/ | Demonstrates the use of laser microdissection (LM) technology for analyses of global gene expression. |
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11 | SEA- Serial Expression Analysis http://sea.bioinfo.cipf.es/ | Web-based resource suite for the analysis of serial transcriptomics data, which offers five different algorithms based on univariate, multivariate and functional profiling strategies . |
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12 | CPAS Not available | Trans-omics pathway analysis tool for jointly analyzing DNA copy number variations and mRNA expression profiles data. |
| | URL can be obtained by sending request to the author. URL can be obtained by sending request to the author |
13 | AtMIAMExpress http://sourceforge.net/projects/miamexpress/ | Open-source web-basedA0softwareA0application to submit Arabidopsis-based microarray data to ArrayExpress and allow export features also. |
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14 | 5'SAGE http://5sage.gi.k.u-tokyo.ac.jp/ | Displays the observed frequencies of individual 5' end SAGE tags and previously unknown transcription start sites in the promoter regions, introns and intergenic regions of known genes. |
| | URL not working as on May 16, 2015 |
15 | AAIR http://aair.cimed.ike.liu.se/ | Provides information about mRNA expression levels of genes of interest in selected microarray studies, relevant to allergic airway inflammation. Two kinds of analyses can be performed, expression analysis and gene search. |
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16 | Ace-it- Array CGH Expression integration tool http://ibivu.cs.vu.nl/programs/acewww/ | Links the chromosomal position of the gene dosage measured by array CGH to the genes measured by the expression array. ACE-it uses this link to statistically test whether gene dosage affects RNA expression. |
| | URL not working as on May 16, 2015 URL not working as on May 16, 2015 |
17 | Adamant http://microarraykit.sourceforge.net/ | Adamant is a java application for annotation of microarray array designs. MIAME-compliant annotation of sequences spotted onto arrays and can produce output files in MAGE-ML and other data formats used by public microarray data repositories. |
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18 | aeGEPUCI http://www.aegep.bio.uci.edu/ | A database of Gene Expression in Dengue vector Mosquito, aeGEPUCI that integrates 1) microarray analyses of sex- and stage-specific gene expression in Ae. aegypti, 2) functional gene annotation, 3) genomic sequence data, and 4) computational sequence analysis tools. |
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19 | AffyMAPSDetector http://www.binf.gmu.edu/weller/BMC_bioinformatics/AffyMapsDetector/ | A software tool to characterize Affymetrix GeneChip expression arrays with respect to SNPs. |
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20 | AGEMAP -Atlas of Gene Expression in Mouse Aging Project http://cmgm.stanford.edu/~kimlab/aging-mouse/ OR www.grc.nia.nih.gov/branch/rrb/dna/agemap_db.htm | Gene expression database, which catalogs expression changes for 8,932 genes in 16 tissues with respect to mice age. |
| | The second URL is not working as on May 16, 2015 The second URL is not working as on May 16, 2015 |
21 | ALE-HAS http://bioinfo.na.iac.cnr.it/ALE-HSA21/ | Integrated and relational database, which provides detailed information about various aspects of genes mapping on chromosome 21, such as gene structure, expression, nucleotide variations and association to diseases. |
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22 | Algal Function Annotation tool http://pathways.mcdb.ucla.edu/algal/index.html | A comprehensive web-based analysisA0suiteA0integrating annotation data from Chlamydomonas reinhardtii and several pathway, ontology, and protein family databases. |
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23 | ABADV- Allen Brain Atlas-Driven Visualizations http://www.socsci.uci.edu/~jkrichma/ABADV/ | Retrieves and visualizes expression energy data from the Allen Brain Atlas (ABA) across multiple genes and brain structures. |
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24 | AMEN-Annotation, Mapping, Expression and Network http://amen.sourceforge.net/ | A stand-alone, unified suite of tools to manage, explore and combine high-throughput data such as annotation, chromosomal location, expression and interaction data. |
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25 | ANEXdb http://www.anexdb.org/ | Open-source web application, which integrates access of two databases- microarrayA0expression(ExpressDB) and EST annotation (AnnotDB) data. |
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26 | angaGEDuCI http://www.angaged.bio.uci.edu/ | Anopheles gambiae gene expression database with integrated comparative algorithm for identifying conserved DNA motif in promoter sequences. |
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27 | AnimalTFDB2 http://bioinfo.life.hust.edu.cn/AnimalTFDB/ | A comprehensive database, classification and annotation of genome-wide transcription factors (TFs), transcription co-factors and chromatin remodeling factors in 65 animal genomes. |
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28 | AnnotationTools http://bioconductor.org/packages/2.1/bioc/html/annotationTools.html | A0Bioconductor-compliant R package for annotation of microarray experiments and integrate heterogeneous gene expressionA0profiles and other molecular biology information. |
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29 | Arabidopsis MPSS http://mpss.udel.edu/#at OR https://mpss.udel.edu/at_mpss2/ | An online resource for quantitative expression analysis for Arabidopsis. |
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30 | ArrayCluster http://www.ism.ac.jp/~higuchi/arraycluster.htm | Freely available software to perform the mixed factors analysis for clustering DNA microarray experiments, data visualization. |
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31 | ArrayProspestor http://www.bork.embl.de/ArrayProspector | Interactive web resource for gene associations predicted by applying a novel algorithm to all expression data in the Stanford Microarray Database. |
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32 | Asterias http://bioinformatics.org/asterias/wiki/Main/DownloadPage | Open-source, web-based, suite for the analysis of gene expression and aCGH data using statistical methods. |
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33 | AtCAST3 http://atpbsmd.yokohama-cu.ac.jp/cgi/atcast/home.cgi | Web-based tool for analysis and comparison of profiles from transcriptome data. Finds stimuli, which induces similar gene expression responses and similar biological processes. |
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34 | AtGenExpress https://www.arabidopsis.org/portals/expression/microarray/ATGenExpress.jsp | Resource designed to find out the transcriptome of the multicellular model organism Arabidopsis thaliana by effort and collaboration of multinational organisation. |
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35 | ATHENA- Analysis Tool for Heritable and Environmental Network Associations http://ritchielab.psu.edu/software/athena-downloads | Integrate high-throughput SNPs and gene expression variables (EVs) to predict high-density lipoprotein cholesterol (HDL-C) levels. |
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36 | Attie Lab Diabetes Database http://diabetes.wisc.edu/ | Allows you to search gene expression in 6 key tissues as a function of obesity, strain, and age, in a mouse model of type II diabetes. |
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37 | AUREA- Adaptive Unified Relative Expression Analyzer http://price.systemsbiology.net/AUREA/ | Cross-platform tool with a consistent application programming interface (API), graphical user interface (GUI), fast running times and automated parameter discovery. |
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38 | Axeldb or Xenbase http://www.xenbase.org/entry/ | Stores and integrates geneA0expressionA0patterns and DNA sequences identified in a large-scale in-situ hybridization study in Xenopus laevis embryos. |
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39 | BarleyBase http://www.plexdb.org/plex.php?database=Barley | Online database for plant microarrays with visualization and statistical analysis tools. Contains raw and normalized expression data from Barley1 and Arabidopsis ATH1. |
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40 | BayBoots http://www.vision.ime.usp.br/~rvencio/BayBoots/ | Freely available web-based tool, which uses a model free baysesian approach to identify class marker from gene expression data. |
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41 | BGEM- Mousebrain Gene Expression Map http://www.stjudebgem.org/ | Provides data on in-situ hybridization images of gene expression patterns in the nervous system of the developing and adult C57BL/6 mouse. |
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42 | Bioclock http://www3.nd.edu/~bioclock/ | Searchable repository of diel and circadian microarray expression data. |
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43 | BioCloneDB http://bioclonedb.agri.huji.ac.il/ | User-friendly database with web interface to assist molecular genetics laboratories in managing a local repository of sequence information linked to DNA clones. |
| | URL not working as on May 16, 2015 URL not working as on May 16, 2015 |
44 | BioMart version0.7 http://biomart.emouseatlas.org/ | Generic data management system which offers a range of advanced query interfaces and administration tools.A0BioMart interface extends access to EMAGE via a powerful method of structuring complex queries. |
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45 | BioXpress v1-0 https://hive.biochemistry.gwu.edu/tools/bioxpress/ | GeneA0expressionA0and cancer associationA0databaseA0withA0expressionA0levels mapped to genes using RNA-seq data The Cancer Genome Atlas, International Cancer Genome Consortium,A0ExpressionA0Atlas and publications. |
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46 | Bladder Cancer Database http://bladder.nhri.org.tw/ | This cDNA sequence database contains 791 sequences that are obtained by nucleotide sequence analysis of cDNA clones randomly isolated from six different cDNA libraries constructed with bladder tumor cell lines or tissues. |
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47 | BodyMap http://bodymap.ims.u-tokyo.ac.jp | |