Tag: dna microarray

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

The Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. In addition to dat ...

Investigation Study Assay Tabular (ISA-Tab) describes the ISA Abstract Model reference implementation specified using the ISA-Tab format. ISA-Tab files are tab separated value (tsv) files, with specific labeled column structures. The ISA model consis ...

Using Simple Omnibus Format in Text (SOFT), researchers can readily upload and download data. The resource is text-based so can be compatible with simple spreadsheets and data applications. A SOFT file can simultaneously contain both tabulated data a ...

MIAME is intended to specify all the information necessary for an unambiguous interpretation of a microarray experiment, and potentially to reproduce it. MIAME defines the content but not the format for this information.

ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Expe ...

The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, related to autism, taken from publicly available literature, databases and unpublished data.

FlyAtlas 2 is the RNA-Seq successor to the original FlyAtlas (which was based on microarray analysis). Specifically, FlyAtlas 2 now provides access to: transcript information, sex-specific data for adult somatic tissues, and micro-RNA genes. FlyAtlas ...

Part of the Progenetix project, the arrayMap database facilitates the study of the genetics of human cancer. The Progenetix project provides the data customisation and visualization tools to mine the available data. The arrayMap database is developed ...

The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With 30817 cases from 1016 publications (Oct 2013), Progenetix is the largest curated database for who ...

Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the FGED Society. However, the complexity of the MAGE-ML format has made its u ...

The Princeton University MicroArray database (PUMAdb) stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, PUMAdb provides interfaces for data retrieval, analysis and visualization.

ToxoDB is a free online resource that provides access to genomic and functional genomic data for Toxoplasma and related organisms. The resource contains over 30 fully sequenced and annotated genomes, with genomic sequence from multiple strains availa ...

MIAME/Plant is a standard describing which biological details should be captured for describing microarray experiments involving plants. Detailed information is required about biological aspects such as growth conditions, harvesting time or harvested ...

TISSUES is a weekly updated web resource that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. All evidence to common protein identifiers and Brenda Tissue O ...

MIAME defines a conceptual structure for defining the core information that is common to most microarray experiments. MIAME/Env is an extension of these guidelines to cover environmental genomics.

Genomic Expression Archive (GEA) is a public database of functional genomics data such as gene expression, epigenetics and genotyping SNP array. Both microarray- and sequence-based data are accepted in the MAGE-TAB format in compliance with MIAME and ...

BarleyBase is a public data resource of Affymetrix GeneChip data for plants.

Annmap is a genome browser that includes mappings between genomic features and Affymetrix microarrays. This resource has been marked as Uncertain because its project home can no longer be found. Please get in touch if you have any information about t ...

The Longhorn Array Database (LAD) is a MIAME‐compliant microarray database that operates on PostgreSQL and Linux. It is a free, completely open‐source, and provides a systematic and proven environment in which vast experiment sets can be safely archi ...

MINiML (MIAME Notation in Markup Language, pronounced 'minimal') is a data exchange format optimized for microarray gene expression data, as well as many other types of high-throughput molecular abundance data. MINiML assumes only very basic relation ...

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.

OmicsDB offers an integrated platform for studying biological networks in multiple organisms, as well as accessing gene expression data. By expanding the classic single species databases across species, it is possible to leverage the amount of inform ...

The GenePix Results Format (GPR) contains general information about microarray image acquisition and analysis, as well as the data extracted from each individual feature. It was originally developed as the output format for GenePix software.