Databases

This section contains databases of microarray data and other gene expression data.

Found 34 links

Displaying 15 links

Adabidopsis eFP BrowserDatabase Content

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An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets (using example of Arabidopsis). Explores microarray and other data for hypothesis generation. eFP Browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets.

ArrayExpress updateDatabase Content

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The ArrayExpress Archive is a public repository of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy.

BgeeDatabase Content

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Bgee is a dataBase for Gene Expression Evolution. It allows one to automatically compare gene expression patterns between species, by referencing expression data on anatomical ontologies, and designing homology relationships between them.

This content is being maintained by bgee.

BioSample DatabaseDatabase Content

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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

Bug@SbaseDatabase Content

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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.

CaSNPDatabase Content

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CaSNP database for storing and interrogating quantitative copy number alterations (CNA) data from SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, CaSNP will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study, and provide links to download the data or visualize it in UCSC Genome Browser. CaSNP also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization.

CellBaseTool Content

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CellBase is a relational database that contains relevant biological information about genomic features and proteins, gene expression regulation, functional annotation, genomic variation and systems biology information. Integrated are the most relevant repositories such as Ensembl, Uniprot, Omim, COSMIC, IntAct, HapMap, Reactome, and others.

This content is being maintained by imedina.

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TitlePublication YearGoogle Scholar Citation Count

COXPRESdbDatabase Content

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COXPRESdb (coexpressed gene database) represents the coexpression relationship for human and mouse. Upgrades include a new comparable coexpression measure, Mutual Rank, five other animal species, rat, chicken, zebrafish, fly and nematoda, and addition of different layers of omics data into the integrated network of genes.

CyclebaseDatabase Content

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Cyclebase is an online resource of cell-cycle-related experiments. This database provides an easy-to-use web interface that facilitates visualization and download of genome-wide cell-cycle data and analysis results. Data from different experiments are normalized to a common timescale and are complimented with key cell-cycle information and derived analysis results. Included is information on cyclin-dependent kinase (CDK) substrates, predicted degradation signals and loss-of-function phenotypes from genome-wide screens. The web interface provides a single, gene-centric graph summarizing the available cell-cycle experiments. Links to orthologous and paralogous genes are included to further facilitate comparison of cell-cycle regulation across species.

Database for Bacterial Group 2 IntronsDatabase Content

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Database for Bacterial Group 2 Introns: a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. General info on group 2 intron properties, structures and classification. Lists info for individual introns (insertion sites, DNA sequences, intron-encoded protein sequences, RNA secondary structure models). Tools fo ridentification and analysis of intron sequences.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
Database for bacterial group II introns20121

EMAGEDatabase Content

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EMAGE is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Data coverage has been increased by sourcing from a greater selection of journals.

ENCODE DCCDatabase Content

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The ENCODE project has a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) serves as the central repository for ENCODE data. The DCC contains a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser. ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay.

FANTOMDatabase Content

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The Functional Annotation Of the Mammalian Genome (FANTOM) is a database for the transcriptional network that regulates macrophage differentiation. Data comes from cap analysis of gene expression (CAGE), sequencing mRNA 5'-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP-chip for epigenetic marks and transcription factors.

Filamentous Fungal Gene Expression Database (FFGED)Database Content

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The filamentous fungal gene expression database (FFGED) is a user-friendly management of gene expression data, which are assorted into experimental metadata, experimental design, raw data, normalized details, and analysis results. FFGED functions as a collective and collaborative platform, by connecting each experiment with similar related experiments made public by other users, and correlating diverse gene expression levels under multiple experimental designs within different experiments.

This content is being maintained by Jeffrey P. Townsend.

GemmaDatabase Content

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Gemma is an open source database, analysis software system and web site for expression data re-use and meta-analysis. It currently contains analyzed data from over 3300 expression profiling studies, yielding billions of data points that can be searched and explored. Gemma offers web-based access to differential expression results and coexpression data in a meta-analysis framework.

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