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.	50
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.	61	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.	64
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.	88	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.	91
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.	94
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.	94	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.	96
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.	98
10	SAM- Shoot Apical Meristem http://sam.truman.edu/	Demonstrates the use of laser microdissection (LM) technology for analyses of global gene expression.	98
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 .	98
12	CPAS Not available	Trans-omics pathway analysis tool for jointly analyzing DNA copy number variations and mRNA expression profiles data.	100	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.	100
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.	100	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.	100
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.	100	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.	100
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.	100
19	AffyMAPSDetector http://www.binf.gmu.edu/weller/BMC_bioinformatics/AffyMapsDetector/	A software tool to characterize Affymetrix GeneChip expression arrays with respect to SNPs.	100
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.	100	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.	100
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.	100
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.	100
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.	100
25	ANEXdb http://www.anexdb.org/	Open-source web application, which integrates access of two databases- microarrayA0expression(ExpressDB) and EST annotation (AnnotDB) data.	100
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.	100
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.	100
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.	100
29	Arabidopsis MPSS http://mpss.udel.edu/#at OR https://mpss.udel.edu/at_mpss2/	An online resource for quantitative expression analysis for Arabidopsis.	100
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.	100
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.	100
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.	100
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.	100
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.	100
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.	100
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.	100
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.	100
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.	100
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.	100
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.	100
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.	100
42	Bioclock http://www3.nd.edu/~bioclock/	Searchable repository of diel and circadian microarray expression data.	100
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.	100	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.	100
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.	100
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.	100
47	BodyMap http://bodymap.ims.u-tokyo.ac.jp	BodyMap is a human and mouse gene expression database that has been maintained since 1993. It is based on site-directed 3 2-ESTs collected from non-biased cDNA libraries constructed at Osaka University and contains >270 000 sequences from 60 human and 38 mouse tissues.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
48	Botany Array Resource(BAR) http://bar.utoronto.ca/welcome.htm	Botany Array Resource or BioAnalytic Resource for Plant Biology is a collection of user-friendly web-based tools for working with functional genomics and other data.	100
49	BrainTrap http://braintrap-karenin.inf.ed.ac.uk/braintrap/	An online database of 3D confocal datasets showing reporter gene expression and protein localization in the adult brain of Drosophila.	100
50	BRB-ArrayTools Data Archive for Human Cancer Gene Expression http://linus.nci.nih.gov/~brb/DataArchive.html	A comprehensive state-of-the-art statistical analysis system for the analysis of microarray gene expression data. It contains numerous analysis tools, including SAM, multivariate permutation tests, classification analysis with complete cross-validation, survival prediction analysis and gene set enhancement analysis.	100
51	B¼G@Sbase http://bugs.sgul.ac.uk/bugsbase/	A microbial geneA0expressionA0and comparative genomicA0database, expertly curated, contains MIAME-compliantA0data that stores comprehensive experimental annotation and multiple raw and analysed data formats.A0	100
52	CAFE https://bitbucket.org/cob87icW6z/cafe/wiki/Home	R package for the detection of gross chromosomal abnormalities from gene expression microarray data.	100
53	CALIB http://bioconductor.org/packages/release/bioc/html/CALIB.html	Bioconductor package for normalization of two-color microarray data.	100
54	CARPET - Collection of Automated Routine Programs for Easy Tiling http://bio.ifom-ieo-campus.it/galaxy	Set of Perl, Python and R scripts, integrated on the Galaxy2 web-based platform, for the analysis of ChIP-chip andA0expressionA0tiling data, both for standard and custom chip designs.	100
55	CDT-DB -Cerebellar Development Transcriptome Database( BrainTx) http://www.cdtdb.neuroinf.jp/CDT/Top.jsp	Spatio-temporal gene expression database collected using in-situ hybridization for spatial resolution and fluorescence differential display, GeneChip, microarray and RT-PCR for temporal resolutio, and were annotated using Gene Ontology and anatomical context. BrainTx was developed from theCDT-DB.	100
56	CellMinerHCC http://medicalgenomics.org/cellminerhcc	A microarray-based expression database for hepatocellular carcinoma cell (18 HCC) lines.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
57	CGED - Cancer gene expression database http://cged.hgc.jp/english/	Expression database obtained from high-throughput RT-PCR technique of solid tumors such as breast, colorectal and hepatocellular cancers.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
58	CHESS (CgHExpreSS) http://biostone.khu.ac.kr/CHESS/	Java-based program, which allows integrative analysis of two experimental data sets: genomic alteration and genome-wideA0expressionA0profile. It comprises of a genomic alteration analysis module and an integrative analysis module.	100
59	CircaDB http://bioinf.itmat.upenn.edu/circa/	Provides circadian transcriptional profiles from time courseA0expressionA0experiments from mice and humans.A0	100
60	CNAmet http://csbi.ltdk.helsinki.fi/CNAmet/	CNAmetA0is an algorithm and R package to prioritize putative cancer driver genes by integrating copy number, DNA methylation and expression data. Outputs of our algorithm include scores for methylation alteration induced expression, copy number aberration induced expression, a score for their combined effect, and adjacent p-values, which are also multiple hypothesis corrected.	100
61	CodeLink http://bioconductor.org/packages/release/bioc/html/codelink.html	R-package for reading and analyzing data from GE Healthcare Gene Expression Bioarrays.	100
62	CoLIde http://srna-workbench.cmp.uea.ac.uk/tools/analysis-tools/colide/	BioinformaticsA0toolA0for CO-expression-based small RNA Loci Identification using high-throughput sequencing data by combining genomic location with the analysis of other information such as variation in expression levels (expression pattern) and size class distribution.	100
63	compcodeR http://master.bioconductor.org/packages/release/bioc/html/compcodeR.html	An R package for benchmarking of differential expression analysis methods, in particular, methods developed for analyzing RNA-seq data.	100
64	CplexA http://sourceforge.net/projects/cplexa/	A MathematicalA0packageA0that uses functional programming to efficiently compute probabilities and average properties over such exponentially large number of states from the energetics of the interactions.	100
65	CressExpress http://cressexpress.org/	User-friendly, online, coexpression analysisA0toolA0for Arabidopsis microarrayA0expressionA0data that computes patterns of correlatedA0expressionA0between user-entered query genes and the rest of the genes in the genome.	100
66	CYPedia -Cytochrome P450 Expression Database http://www-ibmp.u-strasbg.fr/~CYPedia/	A comprehensive database of P450 gene expression based on public Affymetrix ATH1 microarray expression data in four data sets: organs and tissues, stress response, hormone response, and mutants of Arabidopsis thaliana.	100
67	DBATE - DataBase of Alternative Transcripts Expression http://bioinformatica.uniroma2.it/DBATE/	A web-basedA0repositoryA0storingA0expressionA0values and functional annotation of alternative splicing variants.A0	100
68	DCGL http://cran.r-project.org/web/packages/DCGL/index.html or http://lifecenter.sgst.cn/main/en/dcgl.jsp	An R package for differential co-expression analysis (DCEA) and differential regulation analysis (DRA). It contains four modules: 1) gene filtration; 2) link filtration; 3) differential co-expression analysis and 4) differential regulation analysis:	100
69	DepthTools http://cran.r-project.org/web/packages/depthTools/index.html	DepthTools implements different statistical tools for the description and analysis of gene expression data based on the concept of data depth	100
70	DGAP - Diabetes Genome Anatomy Project http://diabetesgenome.org/	The Diabetes Genome Anatomy Project (DGAP) represents a unique, multidimensional initiative whose goal is to unravel the interface between insulin action, insulin resistance and the genetics of type 2 diabetes.	100
71	dGCR http://www.spied.org.uk/cgi-bin/dGCR.cgi	TheA0database ofA0GeneA0Co-Regulation (dGCR) is a web tool for the analysis of gene relationships based on correlated patterns of gene expression over publicly available transcriptional data.	100
72	DGEM http://dgem.dhcp.iupui.edu/	Provides Affymetrix oligonucleotide array datasets for more than 40 human diseases and 1400 samples.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
73	dictyExpress http://dictyexpress.biolab.si/	Provides a graphical, highly interactive explorative interface, which comprises of more than 1000 Dictyostelium discoideum geneA0expressionA0experiments.	100
74	Disease-specific Imaging Probe Profiling (DIPP) Database http://www.polyu.edu.hk/bmi/dipp/	Gene expression profiles validated with a clinical positron emission tomography (PET) study on lung cancer and different diseases, anatomic regions, and subcellular locations, providing an objective reference for selecting imaging probes; an in vitro study on neuroendocrine cancer.	100
75	DR-Integrator http://pollacklab.stanford.edu/software.html	A0A statisticalA0softwareA0toolA0to perform integrative analyses on paired DNA copy number and geneA0expressionA0data.	100
76	DSGeo Not available	Collection of valuable tools that were developed for annotating, aggregating, integrating, and analyzing data deposited in GEO. The core set of tools include a RelationalA0Database, a Data Loader, a Data Browser, and anA0ExpressionA0Combiner and Analyzer.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
77	EDGEdb http://edgedb.umassmed.edu/	Contains sequence information of: i) regulatory elements, including gene promoters, ii) 934 predicted transcription factors, their DNA binding domains, iii) protein-DNA interactions and iv) expression patterns conferred by regulatory elements.	100
78	edgeR http://bioconductor.org/packages/release/bioc/html/edgeR.html	A softwarepackageA0for examining differentialA0expressionA0of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability.	100
79	edgeRun http://cran.r-project.org/web/packages/edgeRun/	R-package for the detection of differentially expressed genes between groups of biological conditions, which exploit RNASeq experiment data by using an unconditional exact test.	100
80	EMAGE http://www.emouseatlas.org/emage/	Provides data on in-situ geneA0expressionA0patterns that allows users to perform online queries of mouse developmental geneA0expression.	100
81	Ermine J http://erminej.chibi.ubc.ca/	A multiplatform user-friendly stand-alone software tool for the analysis of functionally-relevant sets of genes in the context of microarray gene expression data.	100
82	EST2uni http://bioinf.comav.upv.es/est2uni	An integrated, highly-configurable EST analysis pipeline and data mining software package that automates the pre-processing, clustering, annotation, database creation, and data mining of EST collections.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
83	ESTOOLS DATA@HAND http://estools.cs.tut.fi/login_es.php	A resource to facilitate exploration of published gene expression array data in stem cell research.	100
84	Eu.GeneAnalyser http://dc-research.eu/tool/9	A stand-alone application for rapid and powerful microarray data analysis in the context of biological pathways of different organisms and pathway ontologies, transparently deals with multiple nomenclature systems and seamlessly integrates data from different sources.	100
85	Eukaryotic Promoter Database, EPD http://www.epd.isb-sib.ch	Database of an annotated, non-redundant collection of eukaryotic Pol II promoters, for which the transcription start site has been determined experimentally.	100
86	GEDAI-Gene Expression Data Analysis Interface http://eurodia.vital-it.ch	Supports the analysis of gene expression data on EURODIA gene expression database.	100
87	EURODIA gene expression database http://eurodia.vital-it.ch	A unique database of geneA0expressionA0measurements performed on beta-cells of three organisms, namely human, mouse and rat.	100
88	EXPath http://expath.itps.ncku.edu.tw/	Database and resource for gene expression profile obtained from microarray data (under various conditions) to derive metabolic pathways for three model plants: Arabidopsis thaliana, Oryza sativa, and Zea mays.	100
89	Expoldb- Expression linked polymorphism database http://expoldb.igib.res.in/expol	A database for gene expression levels variability across individuals, as well as the presence and features of potentially polymorphic (TG/CA)n repeats and functional information on biochemical pathways of the human genes.A0	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
90	Expression Atlas http://www.ebi.ac.uk/gxa/home;jsessionid=450A5A8D336D0B90DFFCA9AD831A7363	TheA0databaseA0consists of selected high-quality microarray and RNA-sequencing experiments from ArrayExpress that have been manually curated, annotated with Experimental Factor Ontology terms and processed using standardized microarray and RNA-sequencing analysis methods.	100
91	ExpressionBlast http://www.expression.cs.cmu.edu/	A search engine for gene expression data; allow comparison with GEO datasets, and find other studies (even across species) that have similar (or opposite) expression patterns to with your results.	100
92	ExProView - Expression Profile Viewer http://www.biochem.kth.se/exproview/	Software tool for analysis of gene expression profiles derived from expressed sequence tags (ESTs) and SAGE (serial analysis of gene expression).	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
93	EdgeExpressDB http://fantom.gsc.riken.jp/4/	A novel database for gene regulation in acute myeloid leukemia, monocyte/macrophage differentiation set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets	100
94	FAST DB http://fast-db.com/fastdb2/frame.html	Bioinformatics suite for the study of expression regulation of human gene product.	100
95	FastGCN http://ibi.zju.edu.cn/software/FastGCN/	An accelerated and optimized tool for constructing gene co-expression networks that can fully harness the parallel nature of GPU (Graphic Processing Unit) architectures.	100
96	FFGED http://bioinfo.townsend.yale.edu/	A user-friendly geneA0expressionA0database, which contains assorted experimental metadata, experimental design, raw data, normalized details, and analysis results.	100
97	FlyAtlas 2 http://flyatlas.gla.ac.uk/flyatlas/index.html	Provides advanced features for exploring how genes are expressed in the tissues ofA0Drosophila melanogaster.	100
98	FlyEX Database http://urchin.spbcas.ru/flyex/	A quantitative atlas on segmentation gene expression at cellular resolution in the Drosophila blastoderm. Supports operations on images of gene expression patterns.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
99	FlyLight http://flweb.janelia.org/cgi-bin/flew.cgi	A resource for manipulating gene expression and analysis of cis-regulatory module in the Drosophilla CNS.	100
100	FlyPrimerBank http://www.flyrnai.org/flyprimerbank	An online database for Drosophila melanogaster gene expression analysis and knockdown evaluation of RNAi reagents.	100
101	FLYTED Not available	FlyTED, the Drosophila Testis Gene Expression Database, is a biological research database for gene expression images from the testis of the fruit fly Drosophila melanogaster.	100
102	GAAS- Gene Array Analyzer Software. http://www.medinfopoli.polimi.it/gaas/	GAAS software supports multi-user efficient management and suitable analyses of large amounts of gene expression data across replicated experiments.	100
103	GCPReg-package http://urchin.spbcas.ru/downloads/GCPReg/GCPReg.htm	A package for registration of quantitative gene expression data. The key task, which this package performs, is the extraction of spatially localized characteristic features of expression patterns.	100
104	GEDAS- Gene Expression Data Analysis Suite http://gedas.bizhat.com/gedas.htm	Stand-alone software for analysis of microarray gene expression data using Visual Basic and Visual C++ programming languages and techniques such as OM, LVQ, k-means, hierarchical clustering, SVM and PCA.	100
105	GEISHA http://geisha.arizona.edu/geisha/	An online repository of in-situ hybridization and corresponding metadata for genes expressed in the chicken embryo during the first six days of development.A0	100
106	GeMDBJ Proteomics- Genome Medicine Database of Japan Proteomics https://gemdbj.nibio.go.jp/dgdb/	Database for proteome data of surgically resected tissues and tissue-cultured cells of various malignancies, as well as the corresponding biological and clinicopathological data.	100
107	GEMS -Gene Expression Metasignatures http://www.nursa.org/nursa/about/GEMS.jsf	Analysis tool to determine a weighted consensus across multiple datasets for the regulation of a gene by acute (0-4 h) or chronic (24 h) treatment with 17 beta-estradiol in MCF-7 cells.	100
108	GEM-TREND http://cgs.pharm.kyoto-u.ac.jp/network/	Web-toolA0for searching geneA0expressionA0data, using gene-expressionA0signatures or geneA0expressionA0ratio data.	100
109	Gene Class http://gdm.fmrp.usp.br/cgi-bin/gc/upload/upload.pl	An interactive web-based tool for functional annotation of SAGE data using the Gene Ontology (GO) database.	100
110	Gene Expression in Tooth http://bite-it.helsinki.fi/	An online database on gene expression in developing dental tissues.	100
111	GENE2DGE http://bighapmap.big.ac.cn/	A PerlA0softwareA0packageA0for gene model renewal with DGE (digital gene expression) data.	100
112	GeneBins http://bioinfoserver.rsbs.anu.edu.au/utils/GeneBins/ OR http://ricedb.plantenergy.uwa.edu.au/about/data/GeneBins_	GeneBinsA0databaseA0currently supports the functional classification ofA0expressionA0data from four Affymetrix arrays; Arabidopsis thaliana, Oryza sativa, Glycine max and Medicago truncatula.	100
113	GeneExpressionSignature http://www.bioconductor.org/packages/release/bioc/html/GeneExpressionSignature.html	R package for the large-scale analysis of gene expression signatures; provides a flexible solution for gene expression signature-based studies, which can be used in biomedical research applications, such as drug repurposing.	100
114	GeneFriends http://www.genefriends.org/	A0An onlineA0databaseA0that allows users to identify co-expressed genes with one or more user-defined genes.	100
115	GeneHub_GEPIS http://research-public.gene.com/Research/genentech/genehub-gepis/index.html	Performs digital expression analysis in human and mouse tissues based on an integrated gene database.	100
116	GeneTime E(chi)pression warper http://www.psb.ugent.be/cbd/papers/gentxwarper/	A tool for alignment, template matching and visualization of gene expression time series.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
117	GENEVESTIGATOR https://genevestigator.com/gv/	Performs meta-analysis of transcriptomes, visualizes gene expression through a large library of biological contexts, facilitates modeling of gene regulatory networks and the identification of specific markers.	100
118	GenoExp https://hive.biochemistry.gwu.edu/tools/bioxpress/	An integrated RNA-seq-derived database of curated gene expression and disease association in which expression levels are mapped to genes using RNA-seq data obtained from The Cancer Genome Atlas.	100
119	GenomicScape http://www.genomicscape.com/	Web tool for visualization and analysis of highthroughput data; allows mining dataset across different microarray platforms, identification of genes differentially expressed between populations, clustering populations and to export results and figures.	100
120	GENT- Gene Expression database of Normal and Tumor tissues http://genome.kobic.re.kr/GENT/	A web-accessible database that provides gene expression patterns across diverse human cancer and normal tissues.	100
121	GENXL http://www.xenbase.org/vize/3DModels/IDX3DGeneViewer.html	JAVA applet, which provides 3D visualization of anatomy and overlapping gene or protein expression pattern.	100
122	GEOGLE http://omics.biosino.org:14000/kweb/workflow.jsp?id=00020	An integrated geneA0expressionA0information resource from GeneA0ExpressionA0Omnibus (GEO), biomedical ontology from Medical Subject Headings (MeSH) and signaling pathway knowledge from sigPathway entries to develop a context miningA0toolA0for geneA0expressionA0analysis.A0	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
123	GEPAS- Gene Expression Profile Analysis Suite. http://transcriptome.ens.fr/gepas/	Comprises of different interconnected modules, which include tools for data pre-processing, two-conditions comparison, unsupervised and supervised clustering and several tests for differential gene expression among different classes, continuous variables or survival analysis.	100
124	GEPdb http://ercsbweb.ewha.ac.kr/GEPdb/main.html	Provides simultaneous interpretation of both genetic risks and potential gene regulatory pathways toward phenotypic outcome by establishing the ternary relationship of genotype-expression-phenotype (GEP).	100
125	Gepoclu - Gene Positional Clustering. http://gepoclu.sourceforge.net/	A suite of Matlab functions for performing positional clustering on genes with optional use of expression data such as what can be obtained from Microarray, EST and qRT-PCR, and PCR.	100
126	GETDB https://kyotofly.kit.jp/stocks/GETDB/getdb.html	An integrated database, which compiles insertion site, expression pattern and mutant phenotype of a large collection (6966) of Gal4 enhancer trap lines generated and analyzed byA0NP Consortium.	100
127	G-FINDer http://www.bioinformatics.polimi.it/GFINDer/	A Web server that aggregates genomic annotations sparsely available in numerous databanks accessible via the Internet and allows performing statistical analysis of functional and phenotypic annotations of gene lists.	100	Website is currently under maintenance.A0 Website is currently under maintenance.
128	Globin Gene Server http://globin.cse.psu.edu/	Provides data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin.	100
129	GOAD www.goad.education OR http://bioinf.nl:8080/GOAD/databaseSelectServlet	An intuitive web-based interface that consists of three features that enable searching, browsing, analyzing, and downloading of the data, (i) differential geneA0expressionA0(DE) analysis, (ii) quantitative geneA0expressionA0(QE) analysis, (iii) search utility, which can be used to find a gene of interest.	100
130	GonadSAGE http://gonadsage.nichd.nih.gov/sage/home.html	A repository of male embryonic gonad transcriptome information derived from Serial Analysis of Gene Expression (SAGE). A total of six male mouse embryonic gonad stages were included in the current version (E10.5, E11.5, E12.5, E13.5, E15.5 and E17.5).	100
131	Gourmet http://gutsc.wustl.edu/GOurmet/	A software package that calculates the distribution of GO terms represented by the genes in an individualexpressionA0profile (EP), clusters multiple EPs based on these integrated GO term distributions, and provides users several tools to visualize and compare EPs.	100
132	GPXdb http://gpxmea.gti.ed.ac.uk	An online resource forA0geneA0expressionA0based studies of a range of macrophage cell types following treatment with pathogens and immune modulators.	100
133	gViz http://urbm-cluster.urbm.fundp.ac.be/webapps/gviz	A0A GraphML network visualization and explorationA0tool. It implements clustering coefficient-based algorithms.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
134	GXD- Gene Expression Database http://www.informatics.jax.org/	A community resource of gene expression information for the laboratory mouse. The database is designed as an open-ended system that can integrate different types of expression data.	100
135	Heatmap Generator http://heatmapgenerator.sourceforge.net/	HeatmapGenerator is a graphical user interface software program written in C++, R, and OpenGL to create customized gene expression heatmaps from RNA-seq and microarray data in medical research.A0	100
136	Hema Explorer http://servers.binf.ku.dk/hemaexplorer/	CuratedA0databaseA0of processed mRNA GeneA0expressionA0profiles (GEPs) that provides an easy display of geneA0expressionA0in haematopoietic cells.	100
137	Hematopoietic Expression Viewer http://www.shawlab.org/he_viewer/	A prototype mobile app for displaying gene expression data using the iOS platform.	100
138	Hematopoietic Fingerprints http://franklin.imgen.bcm.tmc.edu/loligag/	An expression database of stem cells and their progeny to identify candidate factors involved in differentiation and self-renewal.	100
139	Horse Single Nucleotide Polymorphism and Expression Database (HSDB) http://snugenome2.snu.ac.kr/HSDB/	Provides information on the number of unexplored genomic variants in the horse genome including rare variants by using population genome sequences of eighteen horses and RNA-seq of four horses.	100
140	HTSelf http://blasto.iq.usp.br/~rvencio/HTself/	A web-based bioinformaticsA0toolA0that uses an empirically derived criterion to classify differentially expressed gene by combining two widely accepted ideas in microarray analysis: self-self experiments to derive intensity-dependent cutoffs and non-parametric estimation techniques.	100
141	ICGE http://cran.r-project.org/	User-friendly RA0packageA0for cluster analysis: identify the number of clusters using mixed variables: detect whether the data have a cluster structure; identify whether a new unit belongs to one of the pre-identified clusters or to a novel group, and classify new units into the corresponding cluster.	100
142	ImmuCo http://immuco.bjmu.edu.cn/	Database of geneA0Co-expression andA0Correlation inA0Immune cells. Allows analysis of co-expression and correlation between any two genes and includes expression data from 20,283 human(Affymetrix Human Genome U133 Plus 2.0) and 20,963 mouse genes.	100
143	INMEX (integrative meta-analysis of expression data) http://inmex.ca/INMEX/	A user-friendly web-basedA0toolA0designed to support meta-analysis of multiple gene-expressionA0data sets, as well as to enable integration of data sets from geneA0expressionA0and metabolomics experiments.	100
144	International Database of Cancer Gene Expression http://cgap.nci.nih.gov	A suite of informatics tools was designed to facilitate in silico analysis of the gene expression datasets and are available through the NCI Cancer Genome Anatomy Project web site.	100
145	INVEX http://www.invex.ca/INVEX/	INVEX is a novel web-based tool that integrates data analysis with the browse-based technology for data visualization. INVEX has two key features: (i) flexible differentialA0expressionA0analysis for a wide variety of experimental designs; and (ii) interactive visualization within the context of metadata and biological annotations.	100
146	Jcat http://www.jcat.de/	A novel tool to adapt codon usage of a target gene to its potential expression host. JCat is integrated into the PRODORIC database that hosts all required information on the various organisms to fulfill the requested calculations.	100
147	Kahi Kai http://www.kahikai.org/index.php?content=genes	A comprehensive Gene Expression Database for marine invertebrates . The first web-based comparative gene expression database for invertebrates that allows species-specific as well as cross-species gene expression comparisons.	100
148	KaPPA -View4 http://kpv.kazusa.or.jp/	A metabolic pathwayA0databaseA0for representation and analysis of correlation networks of gene co-expressionA0and metabolite co-accumulation and omics data.	100	Due to a server failure, all the KaPPA-View services on the original server (kpv.kazusa.or.jp) have been stopped since June 7, 2014 Due to a server failure, all the KaPPA-View services on the original server (kpv.kazusa.or.jp) have been stopped since June 7, 2014
149	L2L http://depts.washington.edu/l2l/	Database of differentially expressed genes compiled from published mammalian microarray studies and easy-to-use application for mining theA0databaseA0with the user's own microarray data.	100
150	LINE(Long Interspersed Nuclear Element) FUSION GENES http://www.primate.or.kr/eng2/index.html	Detects LINE (Long Interspersed Nuclear Element) expression throughout the human gene database.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
151	LyM bioinfo.de/isb/2007/07/0009/main.html/	Perl-based tool to determine the best factor for changes in theA0expressionA0level for each transcript across two sets of expressionA0libraries using Bayesian framework.	100
152	M2DB- Microarray Meta-analysis DataBase http://metadb.bmes.nthu.edu.tw/m2db/	Manually curatedA0and customized database for microarray experiment performed using human clinical specimensA0with quality-control metrics set for easy querying, interactive retrieval of raw or uniformly pre-processed data.	100
153	NCI/CIT microArray Database - (mAdb) https://madb.nci.nih.gov/	One of the largest collection of microarray data, covering over 22,000 microarray experiments.	100
154	MADE4 http://bioconductor.org/packages/release/bioc/html/made4.html	Microarray ade4(MADE4), is an R-software package that facilitates multivariate analysis of microarray gene-expression data. MADE4 accepts a wide variety of gene-expression data formats.	100
155	MADSCAN- MicroArray Data Suites of Computed Analysis madtools.org	Dynamic, web-accessible resource, which processes raw microarray scan data for filtering, normalizing and scaling of raw microarray expression data in aA0dynamicA0and automatic way.	100
156	MAGIC- MAize Gene expressIon Compendium http://bioinformatics.intec.ugent.be/magic/	(MAGIC) is a web based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium.	100
157	MAGIC database- Modular Approach to a Genomic, Integrated and Comprehensive database http://fungen.org/gene discovery/	Focuses on gene discovery through production and analysis of expressed sequence tags (ESTs), and subsequently on geneA0expressionA0as assessed by both EST clustering and microarrays.	100	URL is not working and the domain is on sale. URL is not working and the domain is on sale.
158	Maize Cellgenomics Database http://maize.jcvi.org/cellgenomics/index.php	A collection of maize marker lines for studying native gene expression in specific cell types and subcellular compartments using fluorescent proteins (FPs).	100
159	MAIZE WALL http://www.polebio.scsv.ups-tlse.fr/MAIZEWALL/	A0MAIZEWALL contains a bioinformatic analysis for each entry and gene expression data that are accessible via a user-friendly interface.	100
160	MarQ http://marq.dacya.ucm.es/	Explores GEO experiments to identify conditions that induce similar or opposite geneA0expressionA0patterns to a given experimental condition.	100
161	MASISH http://masish.uab.cat/masish/	Provides information on the spatial patterns of gene expression from the high-throughput experiment using maize seedsA0in-situA0hybridization.	100
162	MDCS http://mips.helmholtz-muenchen.de/proj/mdcs/	Microarray Data Classification Server(MDCS)is a web portal for classification of tumor samples based on microarray expression data using MAximal MArgin Linear Programming (MAMA) method.	100
163	MedeiPIEx http://www.cebitec.uni-bielefeld.de/mediplex	Provides information on different sets ofA0expressionA0data generated for the model legume Medicago truncatula.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
164	MENT- Methylation and Expression database of Normal and Tumor tissues http://mgrc.kribb.re.kr:8080/MENT/#main	MENT is an integratedA0databaseA0of DNA methylation and geneA0expression to provide researchers information on both DNA methylation and geneA0expressionA0in diverse cancers.	100
165	MEPD- Medaka Expression Pattern Database http://ani.embl.de:8080/mepd/	A database for gene expression patterns determined by in-situ hybridization in the small freshwater fish medaka (Oryzias latipes).	100
166	mESAdb http://konulab.fen.bilkent.edu.tr/mirna/mirna.php	A database for the multivariate analysis of sequences and expression of microRNAs. It primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets.	100
167	MethHC http://methhc.mbc.nctu.edu.tw/php/index.php	A database comprising a systematic integration of a large collection of DNA methylation data and mRNA/microRNA expression profiles in human cancer.	100
168	Metscape 2 http://metscape.ncibi.org/	A bioinformatics suite for visualization and interpretation of metabolomic and expression profiling data.	100
169	MGDB- Microarray-marker-genes database http://revolutionresearch.uab.es/launcher/gmdb.html	Provides information on the marker genes of all the GEO microarray datasets and is updated monthly with new microarrays from GEO.	100
170	microRNA.org - Targets and Expression http://www.microrna.org/microrna/home.do	A comprehensive resource of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm, which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs.	100
171	MidExDB- Drosophilla CNS Midline Expression database. http://midline.bio.unc.edu/MDB_Home.aspx	Integrates large-scale gene expression data providing the foundation for detailed genetic, molecular, and biochemical studies of CNS midline cell neuronal and glial development and function.	100
172	mirAct http://sysbio.ustc.edu.cn/software/mirAct	Investigates miRNA activity based on gene-expression data by using the negative regulation relationship between miRNAs and their target genes.A0	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
173	MiRGator http://mirgator.kobic.re.kr/	miRGator v3.0 compiled the deep sequencing miRNA data available in public and implemented several novel tools to facilitate exploration of massive data.	100
174	miRNASNP v.2 http://bioinfo.life.hust.edu.cn/miRNASNP2/	Provides information about the expression level and expression correlation of miRNA-related SNPs and target genes in different tissues.	100
175	MirZ http://www.mirz.unibas.ch/	The server provides experimental and computational biologists with statistical analysis and data mining tools operating on up-to-date databases of sequencing-based miRNA expression profiles and of predicted miRNA target sites in species ranging from Caenorhabditis elegans to Homo sapiens.	100	The site is under construction. The site is under construction
176	MIsoMine http://guanlab.ccmb.med.umich.edu/misomine/	Provides data on isoform-level expression, function and network analysis in mouse, allows retrieval of top co-expressed isoforms in diverse tissues and experimental conditions based on the RNA-seq data collected from the Sequence Read Archive (SRA) database.	100
177	MitoGenesisDB http://www.dsimb.inserm.fr/dsimb_tools/mitgene/	Focuses on the dynamics of mitochondrial protein formation by global mRNA analyses and serves as an expressionA0data miningA0toolA0to explore spatio-temporal dynamics of mitochondrial biogenesis.	100
178	MMIA http://epigenomics.snu.ac.kr/MMIA/	This web server will provide life science researchers with a valuable tool for the study of the biological (and pathological) causes and effects of the expression of this class of interesting protein regulators.	100
179	MOPED- Multi-Omics Profiling Expression Database https://www.proteinspire.org/MOPED/mopedviews/proteinExpressionDatabase.jsf	Provides information on transcriptomics relative expression records and has an intuitive user interface with tabs for querying different types of omics expression data and new tools for data visualization.	100
180	MOUSEAC http://www.mouseac.org/	Provides gene expression data from the Mouse Dementia Network i.e, microarray data comparing genome-wide differential expression and pathology throughout life in four lines of "amyloid" transgenic mice (mutant human APP, PSEN1, or APP/PSEN1) and "TAU" transgenic mice (mutant human MAPT gene).	100
181	MtED MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results	An expression database for roots of the model legume Medicago truncatula under salt stress. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results.	100
182	myFX http://www.flyexpress.net/myfx/	A biologist-centric software (myFX) that contains computational methods to automatically process and analyze images depicting embryonic gene expression in the fruit fly Drosophila melanogaster, which interacts directly with the online FlyExpress database.	100
183	National Brain Databank http://www.brainbank.mclean.org/	Provides microarray expression results from postmortem brain tissue samples obtained from the prefrontal cortices of subjects with psychiatric and neurological illness.	100
184	NetPathMiner https://github.com/ahmohamed/NetPathMiner	R/BioconductorA0packageA0for mining network path through geneA0expression and ranks the obtained paths and applies Markov model-based clustering and classification methods to the ranked paths for easy interpretation.	100
185	NRED- Noncoding RNA Expression Database http://nred.matticklab.com/cgi-bin/ncrnadb.pl	Provides geneA0expressionA0information for thousands of long ncRNAs in human and mouse and contains both microarray and in situ hybridization data.	100
186	Okdb- Ovarian Kaleidoscope database http://okdb.appliedbioinfo.net/	Provides information regarding the biological function, expression pattern, and regulation of genes expressed in the ovary as well as for the phenotypes associated with their mutation.	100
187	OncoGenomicsDB https://pob.abcc.ncifcrf.gov/cgi-bin/JK	A web interface for online databases for cancer research funded by National Cancer Institute. It contain a list of Databases and filter option for different parameter.	100
188	Organellar Genome DRAW http://ogdraw.mpimp-golm.mpg.de/	AA0suiteA0ofA0softwareA0tools that enable users to create high-quality visual representations of both circular and linear annotated genome sequences provided as GenBank files or accession numbers.	100
189	Orymold mu.oryzon.com/media/orymold.html	A flexible software application for dynamic gene expression data annotation, integration, and exploration called Orymold.	100
190	OryzaExpress http://bioinf.mind.meiji.ac.jp/OryzaExpress/	A rice database that exploits powerful omics approaches from all perspectives in plant science and leads to systems biology.	100
191	PARE http://proteomics.gersteinlab.org/	Compares protein abundance and mRNA expression data and allows users to select subsets of proteins for focused study (based on functional categories and complexes).	100
192	ParkDB http://www2.cancer.ucl.ac.uk/Parkinson_Db2/	Provides information on geneA0expressionA0in Parkinson's disease and contains a complete set of re-analyzed, curated and annotated microarray datasets.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
193	PathExpress http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/	InterpretsA0gene expressionA0data obtained from microarray experiments by identifying the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes)	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
194	PathMAPA http://dblp.l3s.de/d2r/page/publications/journals/bmcbi/PanSCGMHDZ03	Displays gene expression and performs statistical tests on metabolic pathways at multiple levels for Arabidopsis.	100
195	PathoPlant http://www.pathoplant.de/expression_analysis.php	A novel web tool designated 'in silico expression analysis', which correlates submitted cis-sequences with gene expression data from Arabidopsis thaliana.	100
196	Pathway Processor http://compbiotoolbox.fmach.it/pathwayProcessor/	Visualizes expression data on metabolic pathways and evaluates the metabolic pathways, which are most affected by transcriptional changes in whole-genome expression experiments.	100
197	pca GoPromoter http://bioconductor.org/packages/release/bioc/html/pcaGoPromoter.html	An RA0packageA0for biological and regulatory interpretation of principal components in genome-wide geneA0expressionA0data.	100
198	PCAD- Porcelain Crab Array Database http://online.sfsu.edu/stillmaj/pcad.html	Microarray and transcriptomics database for raw microarray data and sequence homology search results for the porcelain crabA0Petrolisthes cinctipes.	100
199	PEDB (Prostate Expression Database) http://www.pedb.org/	An onlineA0resourceA0designed to access and analyze geneA0expressionA0information derived from the human prostate.	100
200	PEPR- Public Expression Profiling Resource http://pepr.cnmcresearch.org/home.do;jsessionid=B45641A47B72D1141195F68CF2142000	An oracle-based data warehouse containing Affymetrix GeneChip expression profiles of human, mouse and rat. It 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.	100
201	PGS https://github.com/feizhe/PGS	R-package tool for association study of high-dimensional microRNA expression data with repeated measures.	100
202	PhenoGen database http://phenogen.uchsc.edu/	Contains brain microarray data from large panels of inbred, recombinant inbred, selected lines, and genetically modified mice and rats as well as eQTL databases for mice and rats.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
203	PLANdbAffy http://affymetrix2.bioinf.fbb.msu.ru/	Contains the results of the alignment of probe sequences from five AffymetrixA0expressionA0microarrays to the human genome.	100
204	PLANEX (PLAnt co-EXpression database) http://planex.plantbioinformatics.org/	Analyzes plant genes and lists co-expressed genes and functional annotations for Arabidopsis thaliana, Glycine max, Hordeum vulgare, Oryza sativa, Solanum lycopersicum, Triticum aestivum, Vitis vinifera and Zea mays.	100
205	PlantQTL-GE http://www.scbit.org/qtl2gene/new/	A database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
206	PlantTFDB 3.0 http://planttfdb.cbi.pku.edu.cn/	A portal for the functional and evolutionary study of plant transcription factors.	100
207	PlasmoDB http://plasmodb.org/plasmo/	Incorporates finished and draft genome sequence data and annotation emerging from Plasmodium sequencing projects and serves as an official database of the Plasmodium falciparum genome sequencing consortium.	100
208	PLRS- Piecewise Linear Regression Splines http://bioconductor.org/packages/release/bioc/html/plrs.html	Provides information on the association between DNA copy number and gene expression.	100
209	PMTED (Plant MiRNA Target Expression Database) http://pmted.agrinome.org/	Provides information on microRNA (miRNA) functions by inferring their target gene expression profiles, and their target sequences, gene ontology, and differential expression profiles.	100
210	PODC(Plant Omics Data Center) http://bioinf.mind.meiji.ac.jp/podc/	A GeneA0expressionA0network (GEN)A0repository for next-generation sequencing (NGS)-derived from a broad range of plant species.	100
211	POLARMAPPER http://kdbio.inesc-id.pt/software/polarmapper/	A computationalA0toolA0for integrated visualization of protein interaction networks and mRNAexpressionA0data.	100
212	PREGER- Primate Embryo Gene Expression Resource http://www.pregercourse.org/	Analyses gene expression in non-human primate embryos and oocytes.	100
213	PrimerBank http://pga.mgh.harvard.edu/primerbank/	Contains primers that can be used for PCR and qPCR under stringent and allele-invariant amplification conditions and experimental validation of primer pairs covering most known mouse genes. It also contains new primers covering 17,076 and 18,086 genes for the human and mouse species, respectively.	100
214	Proteomic of Oilseeds http://oilseedproteomics.missouri.edu/	A user-intuitive database to access proteomic analysis data, proteome reference maps, expression profiles for soybean, castor and other oilseeds.	100
215	pRRophetic http://genemed.uchicago.edu/~pgeeleher/pRRophetic/ OR https://github.com/paulgeeleher/pRRophetic.	R package that predicts phenotypes or clinical chemotherapeutic response from tumor gene expression levels or expression microarray data.	100
216	READ-RIKEN Expression Array Database http://read.gsc.riken.go.jp/	Provides expression profile data of the mouse cDNA microarray, stores the microarray experimental data and information, and web interfaces for retrieval and analysis.	100
217	RECODE http://recode.genetics.utah.edu/	Compiles 'programmed' translational recoding events from the scientific literature and personal communications. It deals with programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
218	REFOLD http://refold.med.monash.edu.au/	Provides information on the published methods employed in the refolding of recombinant proteins, identifies and optimizes the refolding conditions.	100
219	ReliefSeq http://insilico.utulsa.edu/ReliefSeq.php	A Gene-Wise Adaptive-K Nearest-Neighbor Feature Selection Tool for Finding Gene-Gene Interactions and Main Effects in mRNA-Seq Gene Expression Data.	100
220	REST-Relative Expression Software Tool http://www.gene-quantification.info/	Detection and quantification of mRNA from RT-PCR data and offers high sensitivity, good reproducibility and a wide quantification range.	100
221	RETINOBASE http://alnitak.u-strasbg.fr/RetinoBase	Relational database of microarray, analysis and visualization system about gene expression in retina; provides access to gene expression meta-data and gene networks in retina.	100
222	RGED http://rged.wall-eva.net/	Information on gene expression data from renal disease research; allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys.	100
223	RiceArrayNet http://arraynet.mju.ac.kr/arraynet/	Provides information on coexpression between genes in terms of correlation coefficients (r values) from accumulated microarray data.A0	100
224	RiceDB http://ricedb.plantenergy.uwa.edu.au/	InformationA0portalA0and functional genomicsA0database for Oryza , linking gene loci to comprehensive annotations,A0expression data and the subcellular location of encoded proteins.	100
225	RiceSRTFDB http://www.nipgr.res.in/RiceSRTFDB.html	AA0databaseA0of rice transcription factors containing comprehensiveA0expression for stress responsive, cis-regulatory element and mutant information to facilitate gene function analysis.	100
226	RNASegAtlas http://medicalgenomics.org/rna_seq_atlas	A web-basedA0repositoryA0of RNA-Seq geneA0expressionA0profiles, query tools and offers easy access to RNA-Seq geneA0expressionA0profiles to compare tissues and find out genes with specificA0expressionA0patterns.	100
227	rOGED- rat ovarian gene expression database http://app.mc.uky.edu/kolab/rogedendo.aspx	Database of total RNA isolated from intact ovaries, granulosa cells, or residual ovarian tissues collected from immature pregnant mare serum gonadotropin (PMSG)/human chorionic gonadotropin-treated rats at 0 h (no PMSG), 12 h, and 48 h post PMSG, as well as 6 and 12 h post human chorionic gonadotropin.	100
228	Rosa Chinensis https://lipm-browsers.toulouse.inra.fr/plants/R.chinensis	Transcriptome and Gene Expression atlas for Rose. This web interface allows BLAST, analysis of DNA clusters and access to thorough transcript annotation including best BLAST matches on Fragaria vesca, Prunus persica and Arabidopsis.	100
229	SAGE Genie http://cgap.nci.nih.gov/SAGE	Provides a visual display ofA0humanA0andA0mouseA0gene expression and enhances the interpretation of tag to human gene mapping by incorporation of SNP-associated alternative tags into SAGE Genie.	100
230	SAGEmap http://www.ncbi.nlm.nih.gov/projects/SAGE/ OR ftp://ncbi.nlm.nih.gov/pub/sage	SAGEmap ia a public gene expression data repository and online data access and analysis, WWW and FTP sites for serial analysis of gene expression (SAGE) data.A0	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
231	SBEAMS- Systems Biology Experiment Analysis Management System www.sbeams.org/microarrays/	Open-source, MIAME-compliant storage, management, analysis, and integration of high-throughput genomic expression data. Interoperable with the Cytoscape network integration, visualization, analysis, and modeling software platform.	100
232	SC2 ATmd- Standard and Consensus Clustering Analysis Tool for Microarray Data http://compbiosci.wfu.edu/tools.htm#sc2atmd	MATLAB-implemented application designed for the exploration of microarray gene expression data via clustering tool for microarray data.	100
233	SCADS http://scad.jfcr.or.jp/db/cs/	Gene Expression Database and related analysis tools for evaluation of anticancer compound.	100
234	SCANdb http://www.scandb.org/newinterface/about.html	Large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it.	100
235	SCGAP http://scgap.systemsbiology.net/	Contains gene and protein information for the major cell types of the prostate, prostate cancer cell lines, and a cancer cell type isolated from a primary tumor.	100
236	Scotty http://bioinformatics.bc.edu/marthlab/scotty/scotty.php	Interactive web-based application for statistical design with appropriate sample size and read depth to satisfy the user-defined experimental objectives.	100
237	Seaurchin Embryo Database http://urchin.nidcr.nih.gov/blast/exp.html	A database of mRNA expression patterns for the sea urchin embryo.	100
238	Sebida www.sebida.de OR http://141.61.102.17/sebida/index.php	Database of genes with sex-biased expression integrated from multiple result of independent microarray studies comparing male and female gene expression in Drosophila melanogaster, Drosophila simulans and Anopheles gambiae.	100
239	SEIGE- Smoking Induced Epithelial Gene Expression. http://pulm.bumc.bu.edu/siegeDB	Compiles and analyzes gene expression data from epithelial cells of the human intra-thoracic airway.	100
240	SeqExpress http://www.seqexpress.com/	Useful for the identification of relevant genes within collections of microarray or SAGE experiments.	100
241	SeqGSEA http://bioconductor.org/packages/release/bioc/html/SeqGSEA.html	An open-source Bioconductor package for the functional integration of differential expression and splicing analysis in RNA-Seq data.	100
242	Sequence Searcher http://athena.bioc.uvic.ca/virology-ca-tools/sequence-searcher/	A java tool to perform regular expression and fussy searches of multiple DNA and protein sequences.	100
243	SGD-Saccharomyces Genome Database http://www.yeastgenome.org/	Database for integrated biological information for the budding yeastA0Saccharomyces cerevisiae and analysis tools to explore these data.	100
244	SHIELD: Inner Ear GE db https://shield.hms.harvard.edu/index.html	Database resource for dissemination and comparison of inner-ear gene expression datasets.	100
245	SiPaGene https://www.sipagene.de/sipagene	Repository and a high quality tool for primary analysis of GeneChips. It exploits the MAS5.0/GCOS pairwise comparison algorithm, enables restricted access and user specific sharing.	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
246	SM2miR http://210.46.85.180:8080/sm2mir/index.jsp	Provides a fairly comprehensiveA0repositoryA0about the influences of small molecules on miRNAA0expression, which will promote the development of miRNA therapeutics.	100
247	S-MED- Sarcoma microRNA Expression Database. http://www.oncomir.umn.edu/SMED/index.php	A repositoryA0that describes the patterns of miRNAA0expression, statistical details such as fold changes and P-values for differentially expressed miRNAs in each sarcoma type and corresponding normal human tissue.	100
248	SNPexp http://app3.titan.uio.no/biotools/tool.php?app=snpexp	A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels.	100
249	SoleaDB http://www.juntadeandalucia.es/agriculturaypesca/ifapa/soleadb_ifapa/	Transcriptome database for Solea senegalensis and Solea solea with the assemblies and annotation of new genomic resources from different tissues, developmental stages or stimuli treatments using NGS technologies.	100
250	SolEST database http://biosrv.cab.unina.it/solestdb/	Integrates different EST datasets from both cultivated and wild Solanaceae species and from two species of the genus Coffea.	100
251	SPI http://anti.lab.nig.ac.jp/spi	A tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesis	100	URL not working as on May 16, 2015 URL not working as on May 16, 2015
252	SPIEDw http://www.spied.org.uk/cgi-bin/wSPIED.cgi	Facilitates fast and simple quantitative querying of publically available geneA0expressionA0data.	100
253	SpliceAid 2 www.introni.it/spliceaid.html	Provides information on human splicing factors expression and RNA target motifs; minimizes false positive predictions because it adopts strictly experimental RNA target motifs bound by splicing proteins in humans.	100
254	SplicerAV SplicerAV is freely available upon request from the author.	A tool for mining microarray expression data for changes in RNA processing.	100
255	SplicerEX SplicerEX is freely available upon request from the author.	AA0toolA0for the automated detection and classification of mRNA changes from conventional and splice-sensitive microarrayA0expressionA0data.	100
256	Sscore http://www.bioconductor.org/packages/release/bioc/html/sscore.html	R package for comparison of gene expression between Affymetrix GeneChips using the S-score algorithm based on probe level data directly to assess differences in gene expression, without separate step of probe set expression summary estimation.	100
257	STARNET 2 http://vanburenlab.medicine.tamhsc.edu/starnet2.shtml	Query and visualization tool for precomputed correlation data derived from a large selection of published microarray data and facilitate the development of well-supported hypotheses for gene regulatory influences and signaling pathway topology.	100
258	STEM -Short Time-Series Expression Miner http://www.cs.cmu.edu/~jernst/stem/	A Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments (~8 time points or fewer).A0	100
259	StemBase http://www.stembase.ca/?path=/	Database or Web-interface to DNA microarray data generated by the Canadian Stem Cell Network to facilitate the discovery of gene functions relevant to stem cell control and differentiation.	100
260	SuperFly http://superfly.crg.eu/	A relational database for quantified spatio-temporal expression data of segmentation genes during early development in different species of dipteran insects (flies, midges and mosquitoes).	100
261	SurvExpress http://bioinformatica.mty.itesm.mx:8080/Biomatec/SurvivaX.jsp	A0A cancer-wide geneA0expressionA0databaseA0with clinical outcomes and a web-basedA0toolA0that provides survival analysis and risk assessment of cancer datasets.A0	100
262	SurvJamda- Survival prediction by joint analysis of microarray data http://cran.r-project.org/	R package that uses joint analysis of microarray gene expression data to predict patients' survival and risk assessment.	100
263	svapls : Surrogate variable analysis using partial least squares in a gene expression study http://cran.r-project.org/web/packages/svapls/index.html	Identify genes that are truly expressed differentially over two sample varieties, after adjusting for hidden subject-specific effects of residual heterogeneity.	100
264	SVAw- Surrogate variable analysis Web Service http://psychiatry.som.jhmi.edu/sva/index.php OR http://bioconductor.org/packages/release/bioc/html/sva.html	Web as well as standalone application for surrogate variable analysis of microarray data; user friendly interface for SVA analyses of genome-wide expression studies.	100
265	PviGEA-Switchgrass Functional Genomic Server http://switchgrassgenomics.noble.org/	An integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass. A web server that enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including annotation that helps users formulate hypotheses about gene function.	100
266	TAIR- The Arabidopsis Information Resource https://www.arabidopsis.org/index.jsp	Highly sophisticated and extensive, yet user friendly web-basedA0resourceA0for researchers working on the model plant Arabidopsis thaliana.	100
267	TASE http://tase.sourceforge.net/	Software for fast means of geneA0expression calcutationA0through tag-counts while annotating sequenced reads with the gene's presumed function, from any given CASAVA-build.	100
268	Tbrowser- Transcriptome Browser http://tagc.univ-mrs.fr/tbrowser/	Explores the transcriptional landscape of the GeneA0ExpressionA0OmnibusA0database.	100	JAVA application that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators. JAVA application that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators.
269	TED- Tomato Expression Database http://ted.bti.cornell.edu./	A central repository for raw gene expression data derived from the public tomato cDNA microarray and a collection of tools for analysis and visualization.	100
270	TELIS daatabase -Transcription Element Listening System. telis.ucla.edu	Database which combines sequence-basedA0analysis regulatory regions of ofA0gene with statistical prevalence analyses to identify transcription-factor binding motifs that are over-represented among the promoters of up- or down-regulated genes.	100
271	TGED - Tetrahymena Gene Expression Database http://tged.ihb.ac.cn/	First expression database of a ciliated protozoan. It covers three major physiological and developmental states: growth, starvation, and conjugation, and can be accessed through a user-friendly web interface.	100
272	The Pancreatic Expression Database (PED) http://www.pancreasexpression.org/	Largest collection of multidimensional pancreatic data from the literature including genomic, proteomic, microRNA, methylomic and transcriptomic profiles	100
273	TIBS-Transcriptome of Irritable Bowel Syndrome http://www.chengfeng.info/tibs_database.html	A0Integration of four public expression microarray data (320 samples) from the Gene Expression Omnibus(GEO) and ArrayExpress database.	100
274	TimeCluster http://aimed11.unipv.it/TimeClust/	User-friendly software package to cluster genes according to their temporalA0expressionA0profiles and analyze data obtained from DNA microarray time-course experiments.	100
275	TomatoESTdb http://biosrv.cab.unina.it/tomatestdb/oindex.php	A secondary database integrating expressed sequence tag (EST)/cDNA sequence information from different libraries of multiple tomato species	100
276	TrED- Trichophyton rubrum Expression Database http://www.mgc.ac.cn/TrED/	Provides functional analysis based on GenBank, Pfam, and KOG databases, along with KEGG pathway and GO vocabulary.	100
277	TreeBuilder3D http://www.bcgsc.ca/platform/bioinfo/software/treebuilder/releases/1.0	Visualizes the hierarchical relationships between expression profiles such as SAGE libraries or microarrays.	100
278	UNDO http://www.bioconductor.org/packages/release/bioc/html/UNDO.html	R package for unsupervised deconvolution of tumor and stromal mixed expression data. It detects marker genes and deconvolutes the mixing expression data without any prior knowledge.	100
279	VAMPIRE http://genome.ucsd.edu/microarray/ OR htt://sasquatch.ucsd.edu/vampire/		100
280	ViaComplex http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex/	An open-source application that builds landscape maps of gene expression networks.	100
281	VTCdb http://vtcdb.adelaide.edu.au/Home.aspx	Investigates gene co-expression networks within the cultivated grapevine,A0Vitis vinifera.	100
282	YANA http://yana.bioapps.biozentrum.uni-wuerzburg.de/	Platform-independent software tool for analyzing flux modes, gene-expression and enzyme activities; features dedicated toolbox for metabolic networks with a graphical user interface to calculate, visualize, centralize, and compare elementary flux modes.	100
283	YMD- The Yale Microarray Database http://medicine.yale.edu/keck/ymd/	Database for archiving and retrieving microarray data generated by different labs using different platforms (e.g., Affymetrix, Illumina, Nimblegen and Sequenom).	100
284	yMGV- Yeast Microarray Global Viewer http://www.transcriptome.ens.fr/ymgv/	Provides a synthetic view of the transcriptional expression profiles of yeast genes among most of the published expression datasets.	100
285	YStreX: yeast stress expression database http://www.ystrexdb.com/	Collects, stores and distributes genome-wide expression data generated in the studies of stress responses using yeastA0Saccharomyces cerevisiaeA0as the model organism.	100
286	ZEOGS (Zebrafish Expression Ontology of Gene Sets) http://zeogs.molgen.mpg.de/	A computational method to predict the anatomical region(s) in which changes in expression patterns take place for a given set of input genes.A0	100
287	ZFIN- Zebrafish Model Organism Database http://zfin.org/	A central resource for zebrafish genetic, genomic, phenotypic and developmental data.	100
288	ZODET http://www.ucl.ac.uk/molecular-medicine/key-publications/microarray-outlier-analysis	Provides a user friendly interface that enables identification of gross abnormalities in gene expression (outliers) in individuals with complex disorders, using whole genome microarray data.	100