Provides high-throughput microarray and next-generation sequence (NGS) functional genomic data sets. GEO archives raw data, processed data and metadata submitted by the research community. Its data are indexed, cross-linked and searchable. This database gives access to several tools and graphical renderings allowing users to easily explore and interpret data available on the platform. It can be useful to develop and test new hypotheses.
Provides a database of functional genomics experiments. ArrayExpress includes data generated by sequencing or array-based technologies. This resource integrates 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.
A research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis tools and public data from 300 publications. In addition to supporting ongoing research, SMD makes its source code fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD.
Houses both detailed experimental data and summary of experimental results and provides a convenient query interface and display options for quick retrieval of interesting data. Its applications include archiving data in a queriable manner, finding all experimental results in a targeted genomic locus and assessing biological meaning from high-throughput data.
Provides tools to assist the histologist with array block design and construction. TMAD is an online resource that equips researchers with tissue microarray design tools, image scoring and annotation tools, data sharing mechanisms, an image archive, an analysis toolset and publication mechanism. It also offers a graphical browser to the full ontology with clickable links for browsing to more general or specific terms.
A database that contains the results of the alignment of probe sequences from five Affymetrix expression microarrays to the human genome. In the textual part of the database interface we summarize the data on the sequences that cover the probe alignment region and SNPs that are located inside it. The graphical part of our database interface is implemented as custom tracks to the UCSC genome browser that allows one to utilize all the data that are offered by UCSC browser.
A web-based infrastructure for reliable and secure microarray gene expression data management and analysis that provides an online service for the scientific community. The LCB-DWH is an effort towards a complete system for storage (using the BASE system), analysis and publication of microarray data. Important features of the system include: access to established methods within R/Bioconductor for data analysis, built-in connection to the Gene Ontology database and a scripting facility for automatic recording and re-play of all the steps of the analysis.
Provides a comprehensive MIAME-supportive infrastructure for gene expression data management and makes extensive use of ontologies. Specific details on protocols, biomaterials, study designs, etc. are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format (e.g. ArrayExpress). This infrastructure enables a large variety of queries that incorporate visualization and analysis tools and have been tailored to serve the specific needs of projects focusing on particular organisms or biological systems.
Permits analysis of genes involved in anther and pollen development in order to discover new players during development. FlowerNet has broader application in the characterization of all genes associated with aspects of plant reproduction and flowering. The network has been created using 66 Arabidopsis Affymetrix wild-type microarrays from plant reproduction-related experiments, which included flowers, buds, anther/stamen samples, and isolated pollen samples.
Assists users on human cellular senescence. HCSGD combines multiple online published data sources into a senescence gene annotation platform. Genes are annotated with gene ontology (GO) annotation and microRNA/drug/compound target information. This software provides features like visualization of cellular senescence gene networks, browsing annotated functional information and the recovering senescence-associated genes with a web interface.
Helps user to extract the information on the pathway meta-analysis of metastatic melanoma for the two stages, Cutaneous Metastasis and Lymph Node. M3db contains 642 microarray samples meta-analysed which were used to generate melanoma reconstructed networks representing four different stages of melanoma progression to extract genes with altered molecular circuitry wiring as compared to a normal cellular state. It shows how anti-melanoma drug target efficacy decreases once the melanoma cells program itself for metastasis.
Provides expressed sequence tags (ESTs) currently available from NCBI (Genbank/EMBL/DDBJ) and cassava mRNA sequences and their annotations. Cassava Online Archive simplifies the cassava genomics research and contributes to molecular breeding. It allows to search with sequence similarity (BLAST), accession number and gene function. The annotations collected in this database come from different other protein databases.
Hosts two web applications and one engine. ScreenMill is available online and allows users to obtain quantitative data from high-throughput growth experiments, streamlines the statistical analysis, and offers a novel web-based application to review and visualize data. The three tools are as follows: Colony Measurement Engine (CM Engine) to quantitate colony growth data from plate images; a web-based Data Review Engine (DR Engine) to validate and analyze quantitative screen data, and a web-based Statistics Visualization Engine (SV Engine) to visualize screen data.
Provides a resource that allows different groups performing microarray experiments related to a common subject to create a common coherent knowledge base and to analyse it. The Genopolis database has been implemented as a dedicated system for the scientific community studying dendritic and macrophage cells functions and host-parasite interactions. The Genopolis Database system allows the community to build an object based MIAME compliant annotation of their experiments and to store images, raw and processed data from the Affymetrix GeneChip® platform.
An integrated bioinformatic analytical pipeline to automate the identification of novel candidate cancer markers/targets by means of analysing the expression of user-supplied gene lists across a manually curated database of 80 publicly available cancer microarray datasets and 13 cancer types. Such a meta-analysis enhances reliability and generalizability of the analysis results and leads to a more precise estimate of gene expression. Furthermore, the pipeline facilitates automated, homogeneous and reproducible analysis across a large number of datasets, and establishing a simple-to-use online web interface to access the pipeline puts specialist meta-analyses in the hands of biologists.
Aims to provide a unified and comprehensive resource of information on genes and proteins involved in head and neck (HN) squamous cell carcinoma, covering data on genomics, transcriptomics, proteomics, literature citations and also cross-references of external databases. Different literature searches of MEDLINE abstracts were performed using specific Medical Subject Headings (MeSH terms) for oral, oropharyngeal, hypopharyngeal and laryngeal squamous cell carcinomas. A curated gene-to-publication assignment yielded a total of 1370 genes related to HN cancer. The diversity of results allowed identifying novel and mostly unexplored gene associations, revealing, for example, that processes linked to response to steroid hormone stimulus are significantly enriched in genes related to HN carcinomas. Thus, our database expands the possibilities for gene networks investigation, providing potential hypothesis to be tested.
Provides a gene-centered database of human gene expression. Amazonia! is an atlas that gathers a selection of publicly available transcriptome datasets which can be consulted via thematic pages. The database includes functionalities for allowing users to save personalized lists, customized series of samples, or statistical modules on a personal account. Searches can be made by keywords, Gene identification (ID), UniGene ID or probe ID.
Gathers differential expression profiles of genes expressed in neonatal brains and adult spleen and liver of 129X1/SvJ and C57BL/6J strains of mice. DNA Microarray Database can assist researchers in determining whether a differentially expressed gene is influenced by alterations induced by mutation of the target gene itself or by the genetic background of parent 129X1/SvJ and C57BL/6J mice. The database can also help in predicting the crosses needed to produce a specific gene-targeted mouse.
Provides a repository of probes from Arabidopsis thaliana generated by AnnotationForge. Ath1121501probe includes information about probe sequence, its x et y coordinate on the array, the Affymetrix probe set name, its probe interrogation position and the target strandedness.
Provides a R package that constitutes a repository containing probe sequence for microarrays of barley1. barley1probe furnishes information on probe sequence, its x et y coordinate on the array, the Affymetrix probe set name, its probe interrogation position and the target strandedness.
Provides the service for microarray data storage, retrieval, analysis, and visualization. Access to non-public data is limited to registered University of North Carolina - Chapel Hill researchers and their collaborators.
Provides centralized Affymetrix expression profiling data to the public research community, typically before publication in primary research papers. Data released through PEPR are generated within a single centralized research group (Children’s National Medical Center, Microarray Center), with projects originating internally and referred from external institutions. The web interface enables users to export many forms of data associated with any particular profile, including raw image files (.dat), processed image files (.cel) and interpretation files (.txt). It allows researchers to perform on‐line queries of expression profiles by any number of experimental variables (tissue, species, chip type, etc.).
A web-accessible archive of DNA microarray data. The database was developed using the DNA microarray project /data management system, µArrayDB. Annotations for each DNA microarray project and associated cRNA target information are stored in a MySQL relational database and linked to array hybridization data (raw and normalized). At the discretion of investigators, data are placed into the public domain where they can be interrogated and downloaded through a web browser.
Facilitates workflow management of spotted microarray experiment production, provides an efficient way to gather complete experimental information, and supports collaborative work. In fact, thanks to its well-defined core database architecture, MicroGen facilitates collection and storage of all experimental information according to the MIAME standard. Ordered availability of such information allows subsequent efficient and effective analyses of experimental results. MicroGen also facilitates experimental data comparison. In fact, it allows saving quantitative results also in a standard text format. This increases portability and compatibility of results. Identification of results from experiment with similar characteristic is also facilitated thanks to the complete experimental information orderly stored within the system. MicroGen graphic user interface is very simple and intuitive, providing an easy method for a biologist or a biotechnology technician to read or collect information about performed microarray experiments.
Assists scientists in finding relevant information from published gene expression data. yMGV is a data mining tool coupled to a multi-organism database that currently houses Saccharomyces cerevisiae and Schizosaccharomyces pombe expression data. It provides a global statistical analysis of the expression results. It also offers a graphical representation of the expression changes on the chromosomes, which allows the user to look for physical clusters of co-regulated open reading frame (ORFs).
An online accessible, user-friendly platform dedicated to the biomedical researcher, who is interested in the regulation of gene expression in the human pathogen M. tuberculosis. MycoRegNet's web interface provides the three major capabilities: browsing the database content, searching by specifying filter criteria and basic visualization possibilities. Furthermore, the front-end offers the execution of computational features.
Provides information about gene expression profiles identified in the microorganism, plants, and animals. NABIC Microarray provides three major functions such as microarray search, viewer and download option of raw data. It offers a feature that permits to deposit archive presented as a flexible spreadsheet-based submission format useful for batch deposit of experiments.
Consists of a database schema and Java application for microarray experimental annotation and storage. maxdLoad2 provides several functionalities for browsing, searching and editing data. It permits the visualization of data connectivity, and the ability to explore the links between any pair of data elements, irrespective of how many intermediate links lie between them.
Collects transcription modulation data obtained from microarray experiments Radiation Genes is a relational database that gathers microarrays data from local and public repositories, published papers and supplementary materials. Data is classified in terms of important variables, such as radiation quality, dose, dose rate and sampling timing. The database provides tools to facilitate data integration and comparison. Users can search by gene name, dose quality, dose range and sampling time.