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Total resources - 288
A list of resources for Gene Expression
Thokchom Lellel (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources
Short description*Rank by usage frequency Click to Edit / Add comments
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
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
SOURCE
http://source-search.princeton.edu/
Contains information from a broad range of resources, which are useful for genome-scale analyses.
64
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
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
ROAD - Rice Oligonucleotide Array Database
http://www.ricearray.org/
Database of rice microarray hybridizations and visualization tools for extraction of gene expression profiles using gene and microarray element identifications. It also supports meta-analysis of genes expressed in different tissues and at developmental stages.
94
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
GATE- Grid Analysis of Time series Expression 
http://amp.pharm.mssm.edu/maayan-lab/gate.htm
An integrated computational software platform for the analysis and visualization of high-dimensional biomolecular time series.
96
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
SAM- Shoot Apical Meristem
http://sam.truman.edu/
Demonstrates the use of laser microdissection (LM) technology for analyses of global gene expression.
98
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
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
 AtMIAMExpress
http://sourceforge.net/projects/miamexpress/
Open-source web-based software application to submit Arabidopsis-based microarray data to ArrayExpress and allow export features also.
100
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
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
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
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
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
AffyMAPSDetector
http://www.binf.gmu.edu/weller/BMC_bioinformatics/AffyMapsDetector/
A software tool to characterize Affymetrix GeneChip expression arrays with respect to SNPs.
100
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
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
Algal Function Annotation tool
http://pathways.mcdb.ucla.edu/algal/index.html
A comprehensive web-based analysis suite integrating annotation data from Chlamydomonas reinhardtii and several pathway, ontology, and protein family databases.
100
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
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
ANEXdb
http://www.anexdb.org/
Open-source web application, which integrates access of two databases- microarray expression(ExpressDB) and EST annotation (AnnotDB) data.
100
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
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
AnnotationTools
http://bioconductor.org/packages/2.1/bioc/html/annotationTools.html
 Bioconductor-compliant R package for annotation of microarray experiments and integrate heterogeneous gene expression profiles and other molecular biology information.
100
Arabidopsis MPSS
http://mpss.udel.edu/#at OR https://mpss.udel.edu/at_mpss2/
An online resource for quantitative expression analysis for Arabidopsis.
100
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
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
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
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
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
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
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
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
Axeldb or Xenbase
http://www.xenbase.org/entry/
Stores and integrates gene expression patterns and DNA sequences identified in a large-scale in-situ hybridization study in Xenopus laevis embryos.
100
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
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
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
Bioclock
http://www3.nd.edu/~bioclock/
Searchable repository of diel and circadian microarray expression data.
100
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
BioMart version0.7
http://biomart.emouseatlas.org/
Generic data management system which offers a range of advanced query interfaces and administration tools. BioMart interface extends access to EMAGE via a powerful method of structuring complex queries.
100
BioXpress v1-0
https://hive.biochemistry.gwu.edu/tools/bioxpress/
Gene expression and cancer association database with expression levels mapped to genes using RNA-seq data The Cancer Genome Atlas, International Cancer Genome Consortium, Expression Atlas and publications.
100
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
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
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
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
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
B¼G@Sbase
http://bugs.sgul.ac.uk/bugsbase/
A microbial gene expression and comparative genomic database, expertly curated, contains MIAME-compliant data that stores comprehensive experimental annotation and multiple raw and analysed data formats. 
100
CAFE
https://bitbucket.org/cob87icW6z/cafe/wiki/Home
R package for the detection of gross chromosomal abnormalities from gene expression microarray data.
100
CALIB
http://bioconductor.org/packages/release/bioc/html/CALIB.html
Bioconductor package for normalization of two-color microarray data.
100
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 and expression tiling data, both for standard and custom chip designs.
100
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
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
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
CHESS (CgHExpreSS)
http://biostone.khu.ac.kr/CHESS/
Java-based program, which allows integrative analysis of two experimental data sets: genomic alteration and genome-wide expression profile. It comprises of a genomic alteration analysis module and an integrative analysis module.
100
CircaDB
http://bioinf.itmat.upenn.edu/circa/
Provides circadian transcriptional profiles from time course expression experiments from mice and humans. 
100
CNAmet
http://csbi.ltdk.helsinki.fi/CNAmet/
CNAmet is 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
R-package for reading and analyzing data from GE Healthcare Gene Expression Bioarrays.
100
CoLIde
http://srna-workbench.cmp.uea.ac.uk/tools/analysis-tools/colide/
Bioinformatics tool for 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
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
CplexA
http://sourceforge.net/projects/cplexa/
A Mathematical package that uses functional programming to efficiently compute probabilities and average properties over such exponentially large number of states from the energetics of the interactions.
100
CressExpress
http://cressexpress.org/
User-friendly, online, coexpression analysis tool for Arabidopsis microarray expression data that computes patterns of correlated expression between user-entered query genes and the rest of the genes in the genome.
100
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
DBATE - DataBase of Alternative Transcripts Expression
http://bioinformatica.uniroma2.it/DBATE/
A web-based repository storing expression values and functional annotation of alternative splicing variants. 
100
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
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
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
dGCR
http://www.spied.org.uk/cgi-bin/dGCR.cgi
The database of Gene Co-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
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
dictyExpress
http://dictyexpress.biolab.si/
Provides a graphical, highly interactive explorative interface, which comprises of more than 1000 Dictyostelium discoideum gene expression experiments.
100
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
DR-Integrator
http://pollacklab.stanford.edu/software.html
 A statistical software tool to perform integrative analyses on paired DNA copy number and gene expression data.
100
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 Relational Database, a Data Loader, a Data Browser, and an Expression Combiner and Analyzer.
100

URL not working as on May 16, 2015
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
edgeR
http://bioconductor.org/packages/release/bioc/html/edgeR.html
A softwarepackage for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability.
100
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
EMAGE
http://www.emouseatlas.org/emage/
Provides data on in-situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression.
100
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
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
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
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
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
GEDAI-Gene Expression Data Analysis Interface
http://eurodia.vital-it.ch
Supports the analysis of gene expression data on EURODIA gene expression database.
100
EURODIA gene expression database
http://eurodia.vital-it.ch
A unique database of gene expression measurements performed on beta-cells of three organisms, namely human, mouse and rat.
100
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
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. 
100

URL not working as on May 16, 2015
Expression Atlas
http://www.ebi.ac.uk/gxa/home;jsessionid=450A5A8D336D0B90DFFCA9AD831A7363
The database consists 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
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
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
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
FAST DB
http://fast-db.com/fastdb2/frame.html
Bioinformatics suite for the study of expression regulation of human gene product.
100
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
FFGED
http://bioinfo.townsend.yale.edu/
A user-friendly gene expression database, which contains assorted experimental metadata, experimental design, raw data, normalized details, and analysis results.
100
FlyAtlas 2
http://flyatlas.gla.ac.uk/flyatlas/index.html
Provides advanced features for exploring how genes are expressed in the tissues of Drosophila melanogaster.
100
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
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
FlyPrimerBank
http://www.flyrnai.org/flyprimerbank
An online database for Drosophila melanogaster gene expression analysis and knockdown evaluation of RNAi reagents.
100
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
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
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
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
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. 
100
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
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
GEM-TREND
http://cgs.pharm.kyoto-u.ac.jp/network/
Web-tool for searching gene expression data, using gene-expression signatures or gene expression ratio data.
100
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
Gene Expression in Tooth
http://bite-it.helsinki.fi/
An online database on gene expression in developing dental tissues.
100
GENE2DGE
http://bighapmap.big.ac.cn/
A Perl software package for gene model renewal with DGE (digital gene expression) data.
100
GeneBins
http://bioinfoserver.rsbs.anu.edu.au/utils/GeneBins/ OR http://ricedb.plantenergy.uwa.edu.au/about/data/GeneBins_
GeneBins database currently supports the functional classification of expression data from four Affymetrix arrays; Arabidopsis thaliana, Oryza sativa, Glycine max and Medicago truncatula.
100
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
GeneFriends
http://www.genefriends.org/
 An online database that allows users to identify co-expressed genes with one or more user-defined genes.
100
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
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
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
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
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
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
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
GEOGLE
http://omics.biosino.org:14000/kweb/workflow.jsp?id=00020
An integrated gene expression information resource from Gene Expression Omnibus (GEO), biomedical ontology from Medical Subject Headings (MeSH) and signaling pathway knowledge from sigPathway entries to develop a context mining tool for gene expression analysis. 
100

URL not working as on May 16, 2015
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
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
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
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 by NP Consortium.
100
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. 
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
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 gene expression (DE) analysis, (ii) quantitative gene expression (QE) analysis, (iii) search utility, which can be used to find a gene of interest.
100
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
Gourmet
http://gutsc.wustl.edu/GOurmet/
A software package that calculates the distribution of GO terms represented by the genes in an individualexpression profile (EP), clusters multiple EPs based on these integrated GO term distributions, and provides users several tools to visualize and compare EPs.
100
GPXdb
http://gpxmea.gti.ed.ac.uk
An online resource for gene expression based studies of a range of macrophage cell types following treatment with pathogens and immune modulators.
100
gViz
http://urbm-cluster.urbm.fundp.ac.be/webapps/gviz
 A GraphML network visualization and exploration tool. It implements clustering coefficient-based algorithms.
100

URL not working as on May 16, 2015
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
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. 
100
Hema Explorer
http://servers.binf.ku.dk/hemaexplorer/
Curated database of processed mRNA Gene expression profiles (GEPs) that provides an easy display of gene expression in haematopoietic cells.
100
Hematopoietic Expression Viewer
http://www.shawlab.org/he_viewer/
A prototype mobile app for displaying gene expression data using the iOS platform.
100
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
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
HTSelf
http://blasto.iq.usp.br/~rvencio/HTself/
A web-based bioinformatics tool that 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
ICGE
http://cran.r-project.org/
User-friendly R package for 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
ImmuCo
http://immuco.bjmu.edu.cn/
Database of gene Co-expression and Correlation in Immune 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
INMEX (integrative meta-analysis of expression data)
http://inmex.ca/INMEX/
A user-friendly web-based tool designed to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments.
100
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
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 differential expression analysis for a wide variety of experimental designs; and (ii) interactive visualization within the context of metadata and biological annotations.
100
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
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
KaPPA -View4
http://kpv.kazusa.or.jp/
A metabolic pathway database for representation and analysis of correlation networks of gene co-expression and 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
L2L
http://depts.washington.edu/l2l/
Database of differentially expressed genes compiled from published mammalian microarray studies and easy-to-use application for mining the database with the user's own microarray data.
100
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
LyM
bioinfo.de/isb/2007/07/0009/main.html/
Perl-based tool to determine the best factor for changes in the expression level for each transcript across two sets of expression libraries using Bayesian framework.
100
M2DB- Microarray Meta-analysis DataBase
http://metadb.bmes.nthu.edu.tw/m2db/
Manually curated and customized database for microarray experiment performed using human clinical specimens with quality-control metrics set for easy querying, interactive retrieval of raw or uniformly pre-processed data.
100
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
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
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 a dynamic and automatic way.
100
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
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 gene expression as assessed by both EST clustering and microarrays.
100

URL is not working and the domain is on sale.
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
MAIZE WALL
http://www.polebio.scsv.ups-tlse.fr/MAIZEWALL/
 MAIZEWALL contains a bioinformatic analysis for each entry and gene expression data that are accessible via a user-friendly interface.
100
MarQ
http://marq.dacya.ucm.es/
Explores GEO experiments to identify conditions that induce similar or opposite gene expression patterns to a given experimental condition.
100
MASISH
http://masish.uab.cat/masish/
Provides information on the spatial patterns of gene expression from the high-throughput experiment using maize seeds in-situ hybridization.
100
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
MedeiPIEx
http://www.cebitec.uni-bielefeld.de/mediplex
Provides information on different sets of expression data generated for the model legume Medicago truncatula.
100

URL not working as on May 16, 2015
MENT- Methylation and Expression database of Normal and Tumor tissues
http://mgrc.kribb.re.kr:8080/MENT/#main
MENT is an integrated database of DNA methylation and gene expression to provide researchers information on both DNA methylation and gene expression in diverse cancers.
100
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
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
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
Metscape 2
http://metscape.ncibi.org/
A bioinformatics suite for visualization and interpretation of metabolomic and expression profiling data.
100
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
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
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
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. 
100

URL not working as on May 16, 2015
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
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
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
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
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 expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis.
100
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
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
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
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
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
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
NetPathMiner
https://github.com/ahmohamed/NetPathMiner
R/Bioconductor package for mining network path through gene expression and ranks the obtained paths and applies Markov model-based clustering and classification methods to the ranked paths for easy interpretation.
100
NRED- Noncoding RNA Expression Database
http://nred.matticklab.com/cgi-bin/ncrnadb.pl
Provides gene expression information for thousands of long ncRNAs in human and mouse and contains both microarray and in situ hybridization data.
100
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
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
Organellar Genome DRAW
http://ogdraw.mpimp-golm.mpg.de/
A suite of software tools 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
Orymold
mu.oryzon.com/media/orymold.html
A flexible software application for dynamic gene expression data annotation, integration, and exploration called Orymold.
100
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
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
ParkDB
http://www2.cancer.ucl.ac.uk/Parkinson_Db2/
Provides information on gene expression in 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
PathExpress
http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/
Interprets gene expression data 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
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
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
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
pca GoPromoter
http://bioconductor.org/packages/release/bioc/html/pcaGoPromoter.html
An R package for biological and regulatory interpretation of principal components in genome-wide gene expression data.
100
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 crab Petrolisthes cinctipes.
100
PEDB (Prostate Expression Database)
http://www.pedb.org/
An online resource designed to access and analyze gene expression information derived from the human prostate.
100
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
PGS
https://github.com/feizhe/PGS
R-package tool for association study of high-dimensional microRNA expression data with repeated measures.
100
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
PLANdbAffy
http://affymetrix2.bioinf.fbb.msu.ru/
Contains the results of the alignment of probe sequences from five Affymetrix expression microarrays to the human genome.
100
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
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
PlantTFDB 3.0
http://planttfdb.cbi.pku.edu.cn/
A portal for the functional and evolutionary study of plant transcription factors.
100
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
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
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
PODC(Plant Omics Data Center)
http://bioinf.mind.meiji.ac.jp/podc/
A Gene expression network (GEN) repository for next-generation sequencing (NGS)-derived from a broad range of plant species.
100
POLARMAPPER
http://kdbio.inesc-id.pt/software/polarmapper/
A computational tool for integrated visualization of protein interaction networks and mRNAexpression data.
100
PREGER- Primate Embryo Gene Expression Resource
http://www.pregercourse.org/
Analyses gene expression in non-human primate embryos and oocytes.
100
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
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
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
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
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
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
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
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
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
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
RiceArrayNet
http://arraynet.mju.ac.kr/arraynet/
Provides information on coexpression between genes in terms of correlation coefficients (r values) from accumulated microarray data. 
100
RiceDB
http://ricedb.plantenergy.uwa.edu.au/
Information portal and functional genomics database for Oryza , linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins.
100
RiceSRTFDB
http://www.nipgr.res.in/RiceSRTFDB.html
A database of rice transcription factors containing comprehensive expression for stress responsive, cis-regulatory element and mutant information to facilitate gene function analysis.
100
RNASegAtlas
http://medicalgenomics.org/rna_seq_atlas
A web-based repository of RNA-Seq gene expression profiles, query tools and offers easy access to RNA-Seq gene expression profiles to compare tissues and find out genes with specific expression patterns.
100
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
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
SAGE Genie
http://cgap.nci.nih.gov/SAGE
Provides a visual display of human and mouse gene expression and enhances the interpretation of tag to human gene mapping by incorporation of SNP-associated alternative tags into SAGE Genie.
100
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. 
100

URL not working as on May 16, 2015
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
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
SCADS
http://scad.jfcr.or.jp/db/cs/
Gene Expression Database and related analysis tools for evaluation of anticancer compound.
100
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
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
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
Seaurchin Embryo Database
http://urchin.nidcr.nih.gov/blast/exp.html
A database of mRNA expression patterns for the sea urchin embryo.
100
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
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
SeqExpress
http://www.seqexpress.com/
Useful for the identification of relevant genes within collections of microarray or SAGE experiments.
100
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
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
SGD-Saccharomyces Genome Database
http://www.yeastgenome.org/
Database for integrated biological information for the budding yeast Saccharomyces cerevisiae and analysis tools to explore these data.
100
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
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
SM2miR
http://210.46.85.180:8080/sm2mir/index.jsp
Provides a fairly comprehensive repository about the influences of small molecules on miRNA expression, which will promote the development of miRNA therapeutics.
100
S-MED- Sarcoma microRNA Expression Database.
http://www.oncomir.umn.edu/SMED/index.php
A repository that describes the patterns of miRNA expression, statistical details such as fold changes and P-values for differentially expressed miRNAs in each sarcoma type and corresponding normal human tissue.
100
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
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
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
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
SPIEDw
http://www.spied.org.uk/cgi-bin/wSPIED.cgi
Facilitates fast and simple quantitative querying of publically available gene expression data.
100
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
SplicerAV
SplicerAV is freely available upon request from the author.
A tool for mining microarray expression data for changes in RNA processing.
100
SplicerEX
SplicerEX is freely available upon request from the author.
A tool for the automated detection and classification of mRNA changes from conventional and splice-sensitive microarray expression data.
100
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
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
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). 
100
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
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
SurvExpress
http://bioinformatica.mty.itesm.mx:8080/Biomatec/SurvivaX.jsp
 A cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. 
100
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
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
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
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
TAIR- The Arabidopsis Information Resource
https://www.arabidopsis.org/index.jsp
Highly sophisticated and extensive, yet user friendly web-based resource for researchers working on the model plant Arabidopsis thaliana.
100
TASE
http://tase.sourceforge.net/
Software for fast means of gene expression calcutation through tag-counts while annotating sequenced reads with the gene's presumed function, from any given CASAVA-build.
100
Tbrowser- Transcriptome Browser
http://tagc.univ-mrs.fr/tbrowser/
Explores the transcriptional landscape of the Gene Expression Omnibus database.
100

JAVA application that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators.
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
TELIS daatabase -Transcription Element Listening System.
telis.ucla.edu
Database which combines sequence-based analysis regulatory regions of of gene with statistical prevalence analyses to identify transcription-factor binding motifs that are over-represented among the promoters of up- or down-regulated genes.
100
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
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
TIBS-Transcriptome of Irritable Bowel Syndrome
http://www.chengfeng.info/tibs_database.html
 Integration of four public expression microarray data (320 samples) from the Gene Expression Omnibus(GEO) and ArrayExpress database.
100
TimeCluster
http://aimed11.unipv.it/TimeClust/
User-friendly software package to cluster genes according to their temporal expression profiles and analyze data obtained from DNA microarray time-course experiments.
100
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
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
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
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
VAMPIRE
http://genome.ucsd.edu/microarray/ OR htt://sasquatch.ucsd.edu/vampire/
100
ViaComplex
http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex/
An open-source application that builds landscape maps of gene expression networks.
100
VTCdb
http://vtcdb.adelaide.edu.au/Home.aspx
Investigates gene co-expression networks within the cultivated grapevine, Vitis vinifera.
100
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
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
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
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 yeast Saccharomyces cerevisiae as the model organism.
100
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. 
100
ZFIN- Zebrafish Model Organism Database
http://zfin.org/
A central resource for zebrafish genetic, genomic, phenotypic and developmental data.
100
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
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