Tag: microarray experiment

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 ...

The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in miRBase represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence ...

The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

DIANA-TarBase is a reference database that indexes experimentally-supported microRNA (miRNA) targets. It integrates information on cell-type specific miRNA–gene regulation and includes miRNA-binding locations. The target data provided by DIANA-TarBas ...

A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.

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 ...

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-scal ...

As a database, miRTarBase has accumulated more than fifty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to fu ...

An annotated collection of all publicly available nucleotide and protein sequences. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in other countries. DDBJ is part of the International Nucleotide Sequence Databas ...

The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins.

The GeneWeaver data and analytics website is a publically available resource for storing, curating and analyzing sets of genes from heterogeneous data sources. The system enables discovery of relationships among genes, variants, traits, drugs, enviro ...

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.

miRNA target prediction and functional annotation

ATTED-II is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can find functional gene relationships and design experiments to identify gene functions by reverse gene ...

AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first released, AmoebaDB contained the genomes of three Entamoeba species. AmoebaDB int ...

Database for meta-analysis of the prognostic value of genes. It has features of 1) a large collection of publicly available cancer microarray datasets with clinical annotation, as well as 2) a tool for assessing the biological relationship between ge ...

This resource details DNA methylation profiles in human and mouse brain. This database includes genome-wide DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end ...

miRNEST is an integrative collection of animal, plant and virus microRNA data. miRNEST is being gradually developed to create an integrative resource of miRNA-associated data. The data comes from our computational predictions (new miRNAs, targets, mi ...

The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that b ...

MIRAGE (Minimum Information Required for A Glycomics Experiment was created to improve the quality of glycomics data in the scientific literature. These guidelines were drafted to be intentionally minimal and apply only to information required for ge ...

Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.

Gene expression data sorted into two groups: expressed and not expressed genes

DNMIVD is a comprehensive annotation and interactive visualization database for DNA methylation profile of diverse human cancer constructed with high throughput microarray data from TCGA and GEO databases, and it also integrates some data from Pancan ...

The database integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and ...

The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarra ...

Metabolic gEne RApid Visualizer

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 ...

Public repository for gene expression experimental data. The database system is compliant with the MIAME standard.

MEM (Multi-Experiment Matrix) provides gene expression similarity searches, visualisation and analyses across many datasets from ArrayExpress and GEO. MEM uses rank aggregation to merge information from different datasets into a single global orderin ...

Tissue microarrays (TMA) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential ...

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 ...

Probe-Level Annotation Database for Affymetrix microarrays

Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining targ ...

microRNA Expression and Sequence Analysis Database

The Ashbya Genome Database (AGD) is a genome/transcriptome database containing gene annotation and high-density oligonucleotide microarray expression data for protein-coding genes from Ashbya gossypii and the model organism Saccharomyces cerevisiae.

a database of endothelial cell transcriptomics data. EndoDB The endothelial cell database (EndoDB) is a freely accessible added-value database that facilitates bench scientists to unlock the untapped potential of publicly available (single cell) tra ...

EXPath is a database resource that collects and utilizes expression profiles derived from microarray under various conditions to infer metabolic pathways for six model plants: Arabidopsis thaliana, Oryza sativa, Zea mays, Solanum lycopersicum, Glycin ...

"iModulons", groups of independently-modulated genes

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 ...

A unified gene expression atlas for the model plant Physcomitrella patens. PEATmoss is an interactive tool to visualize gene expression data. These help pages explain several ways to query the expression data and to visualize the results, enabling t ...

Breast cancer gene-expression miner (bc-GenExMiner) 4.5 is a mining module computes breast cancer differential gene expression analyses. It is a statistical mining tool of published annotated breast cancer transcriptomic data (DNA microarrays and RNA ...

FORK-seq is a replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing

BuG@Sbase is a microbial gene expression and comparative genomic database containing microarray datasets.

Restructured version of Gene Expression Omnibus (GEO) that provides a user friendly interface for curating GEO database

The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ...

Systematic investigation of cytokine signaling activity at the tissue and single-cell levels.

Expression data to explore spatio-temporal dynamics of mitochondrial biogenesis

A comprehensive database with multiple animal reference panels for genotype imputation.

Phylogenetic Oligonucleotide Probe Database. Provides a convivial and easy-to-use web interface to browse both regular and explorative 16S rRNA-targeted probes.

Glycan Microarray Database and Analysis Toolset.

Knowledge database of Soybean Functional gene Networks and miRNA functional networks.

Re-annotating oligo sets used for expression microarrays is essential to supply biologists with up-to-date annotations. The tool is a query environment populated with regularly updated annotations for different oligo sets. It permits easy extraction ...

The NimbleGen Gene Description is a text tabular format that contains descriptive information (annotation) about the genes on an array. Please note that Roche issued a statement in 2012 as follows: "As previously announced in June 2012, Roche has exi ...

CNAdbCC is a curated database for copy number aberrations analysis and visualization of cervical cancer. Currently, the database contains about 1,000 dataset samples mainly integrated by affymetrix and aligent platform. Affymetrix is based on light-c ...

A database of experimentally supported protein-coding RNAs and drug associations in human cancer.

TRANSNAP is a web database providing comprehensive information on Japanese pear transcriptome.

A Liver Disease Microarray Database, Visualization Platform and Data-Mining Resource. Providing Bioinformatics Data For The Study Of Liver Diseases. a liver disease microarray database, visualization platform and data-mining resource. Hepamine was ...

Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma.

CoFly is a gene coexpression database for the fruit fly Drosophila melanogaster

A web service for studying gene expression in human skeletal muscle. MuscleAtlasExplorer(BETA)2.

The One-stop Database for COVID-19 Specific Humoral Immunity and Clinical Parameters.

A database of organ-specific metastasis induced by human cancer cell lines in mouse models. The organotropism is the propensity of metastatic cancer cells to colonize preferably certain distant organs, resulting in a non-random distribution of metas ...

A manually curated database for experimentally validated non-coding RNAs in inflammation. Non-coding RNAs in Inflammation (ncRI) provides a manually curated database for experimentally validated non-coding RNAs in inflammatary disease. Recently, inf ...

Haloarchaeal genomes database.

AOE (All Of gene Expression) - an integrated index for public gene expression databases.

A curated repository of cell types with multifaceted characterization.

Powerful new framework for interrogation of global pathway relationships.

The Gene Expression Database of Poplar under Stress.

A blood platelets-based gene expression database for disease investigation.

The Chinese Glioma Genome Atlas (CGGA) is a user-friendly web application for data storage and analysis to explore brain tumors datasets. This database includes the whole-exome sequencing, DNA methylation, mRNA sequencing, mRNA microarray and microRN ...

EpiMOLAS (Epi-genoMics OnLine Analysis System) is an intuitive web-based framework for genome-wide DNA methylation analysis.

dbDEMC (database of Differentially Expressed MiRNAs in human Cancers) is an integrated database that designed to store and display differentially expressed microRNAs cancers detected by high-throughput and low-throughput methods.

Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage.

A Server Platform For High Altitude Human miRNA-Gene Coregulatory Networks And Associated Regulatory-Circuits. HAHmiR DB (High-Altitude Human miRNA Database) is a unique, comprehensive, curated collection of miRNAs that have been experimentally vali ...

Database of transcriptomic profiles of human brains of six neuropsychiatric disorders.

BDdb is a comprehensive database associated with birth-defect-related diseases. It consists of multi-omics datasets involving tens of common birth-defect diseases, and BDdb supplements more than 2000 biomarkers belonging to 22 types of birth defects.

CancerMIRNome is a web server for cancer miRNome interactive analysis and visualization based on the huamn miRNome data of 33 cancer types from The Cancer Genome Atlas (TCGA), and 40 public cancer circulating miRNome profiling datasets from NCBI Gene ...

The One-stop Database for COVID-19-specific Antibody Responses and Clinical Parameters.

A scalable artificial intelligence platform that automatically finds copy number variations (CNVs) in journal articles and transforms them into a database.

Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines | The Cancer Dependency Map Project at Broad Institute | A resource of data and computational tools to expose the vulnerabilities of cancer, and ...

Genome-wide analysis of polymorphisms identified domestication-associated polymorphism desert carrying important rice grain size/weight QTL | By using SNP-Seek, you abide by the data use license stated | Query for SNPs from the 3000 genome project | ...

An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Plasmodium falciparum Community Project. Dried blood spot collection. Photo credit: Will Hamilton. HiSeq machines at the Wellcome Trust Sanger Institute. Photo c ...

An integrative platform for comparative and functional genomics of marmots. iMarmot: an integrative Marmot database. Marmots are large Holarctic rodents in the genus Marmota with 14 living species. Most marmot species occupy a harsh environment cha ...