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AgBaseDatabase Content

http://www.agbase.msstate.edu/ [open in a new window]

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Model Organisms > Databases

AgBase provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
AgBase: supporting functional modeling in agricultural organisms20116
NAR Database Issue 2011
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tagsagricultural crops agriculture animals cats dogs domestic animals gene expression profiling genetic databases genetic models genomics oligonucleotide array sequence analysis

ArrayExpressDatabase Content

http://www.ebi.ac.uk/arrayexpress/ [open in a new window]

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Expression > Transcript Expression Analysis

Public repository for microarray based gene expression data; contains several curated gene expression datasets.

links directory index: 659
TitlePublication YearGoogle Scholar Citation Count
The ArrayExpress gene expression database: a software engineering and implementation perspective200536
Submission of microarray data to public repositories200494
ArrayExpress--a public repository for microarray gene expression data at the EBI2003529
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BioSample DatabaseDatabase Content

http://www.ebi.ac.uk/biosamples/ [open in a new window]

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DNA > Databases
Expression > Databases
Protein > Proteomics

The BioSample Database at the EBI is designed to hold information about biological samples, particularly samples referenced from other EBI databases. BioSD data will be exchanged with NCBI

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
The BioSample Database (BioSD) at the European Bioinformatics Institute20123
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setsEuropean Bioinformatics Institute (EBI)

Bug@SbaseDatabase Content

http://bugs.sgul.ac.uk/bugsbase/ [open in a new window]

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Expression > Databases
Model Organisms > Databases
Model Organisms > Microbes

A relational database containing microbial gene expression and comparative genomic hybridisation experimental data. The data is mostly derived from whole genome microarrays designed by the BµG@S group, however data from other microarrays is included and the database is being modified to support RNA-Seq analysis. Public access is available for datasets that have been published and login credentials can be obtained for data submission.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
BμG@Sbase--a microbial gene expression and comparative genomic database20121
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DDBJDatabase Content

http://www.ddbj.nig.ac.jp [open in a new window]

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DNA > Databases

The DNA Data Bank of Japan (DDBJ) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. A new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Other improvements include improved content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based analytical system from sequencing reads, the DDBJ Read Annotation Pipeline.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments20123
DDBJ progress report201115
DDBJ launches a new archive database with analytical tools for next-generation sequence data201031
NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms amino acid sequence animals bacterial genome computational biology genetic databases genomics humans japan molecular sequence annotation nucleic acid databases patents as topic protein databases

European Nucleotide ArchiveDatabase Content

http://www.ebi.ac.uk/ena [open in a new window]

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DNA > Databases

The European Nucleotide Archive (ENA) is Europe's nucleotide-sequence repository. The ENA consists of three main databases: the Sequence Read Archive (SRA), the Trace Archive and EMBL-Bank. New features include extended EMBL-Bank and SRA-data submission services, extended ENA Browser functionality, support for submitting data to the European Genome-phenome Archive (EGA) through SRA, and the launch of a new sequence similarity search service.

This content is being maintained by rasko.

links directory index: 55
TitlePublication YearGoogle Scholar Citation Count
Major submissions tool developments at the European Nucleotide Archive20121
The European Nucleotide Archive201129
Improvements to services at the European Nucleotide Archive201025
NAR Database Issue 2010NAR Database Issue 2011
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Expression ProfilerTool Content

http://www.ebi.ac.uk/expressionprofiler/ [open in a new window]

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Expression > Transcript Expression Analysis

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

links directory index: 99
TitlePublication YearGoogle Scholar Citation Count
Expression Profiler: next generation--an online platform for analysis of microarray data200499
NAR Web Server Issue 2004NAR Web Server Issue 2005
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tagsgene expression profiling genomics oligonucleotide array sequence analysis

FatiGOplusTool Content

http://www.fatigo.org/ [open in a new window]

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DNA > Annotations
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Networks & Interactions, Pathways and Enzymes

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

links directory index: 1322
TitlePublication YearGoogle Scholar Citation Count
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments2007150
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments2006215
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments2005204
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes2004753
NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs animals artificial intelligence binding sites chromosome mapping computational biology dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny programming languages rats sequence alignment systems biology systems integration transcription factors

Gene Expression AtlasDatabase Content

http://www.ebi.ac.uk/gxa/ [open in a new window]

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Expression > Databases

The Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments20124
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Gene Expression BarcodeDatabase Content

http://rafalab.jhsph.edu/barcode [open in a new window]

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Expression > Databases

Gene Expression Barcode is a database that provides reliable absolute measures of expression for most annotated genes for human and mouse tissue types, including diseased tissue. This is made possible by an algorithm that leverages information from the GEO and ArrayExpress public repositories to build statistical models that permit converting data from a single microarray into expressed/unexpressed calls for each gene. For selected platforms, users may upload data and obtain results.

This content is being maintained by rafelon.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes201113
NAR Database Issue 2011
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tagsanimals gene expression profiling genetic databases humans mice oligonucleotide array sequence analysis

GXADatabase Content

http://www.ebi.ac.uk/gxa [open in a new window]

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Expression > Databases

The Gene Expression Atlas is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data. A simple interface allows the user to query for differential gene expression either (i) by gene names or attributes such as Gene Ontology terms, or (ii) by biological conditions, e.g. diseases, organism parts or cell types.

links directory index: 67
TitlePublication YearGoogle Scholar Citation Count
Gene expression atlas at the European bioinformatics institute201067
NAR Database Issue 2010
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tagsanimals computational biology europe gene expression profiling genetic databases humans nucleic acid databases statistical models

MADNetTool Content

http://www.bioinfo.hr/madnet [open in a new window]

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Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Microarray Database Network (MADNet) is a data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. Data is integrated with information from NCBI, KEGG TRANSFAC and DrugBank.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
MADNet: microarray database network web server20088
NAR Web Server Issue 2008
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tagsgene expression profiling genetic databases metabolic networks and pathways oligonucleotide array sequence analysis signal transduction systems integration

MIAMExpressTool Content

http://www.ebi.ac.uk/microarray/MIAMExpress/miamexpress.html [open in a new window]

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Expression > Transcript Expression Analysis

MIAME (minimum information about a microarray experiment) compliant microarray data submission tool.

links directory index: 529
TitlePublication YearGoogle Scholar Citation Count
ArrayExpress--a public repository for microarray gene expression data at the EBI2003529
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Microarray RetrieverTool Content

http://www.lgtc.nl/MaRe/ [open in a new window]

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Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE

Microarray Retriever (MaRe) is a web tool that enables batch search and retrieval of microarray datasets matching user specified criteria from the data in GEO and ArrayExpress microarray repositories. Such batch download facilitates gene expression meta-analysis.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data200812
NAR Web Server Issue 2008
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NCBI GEODatabase Content

http://www.ncbi.nlm.nih.gov/geo/ [open in a new window]

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Expression > Databases

The Gene Expression Omnibus (GEO) database stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies.

links directory index: 2099
TitlePublication YearGoogle Scholar Citation Count
NCBI GEO: archive for functional genomics data sets--10 years on2011142
Submission of microarray data to public repositories200494
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository20021863
NAR Database Issue 2011
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setsNational Center for Biotechnology Information (NCBI)

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