Tag: microarray data and other gene expression

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 ...

modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

The Expression Atlas is a free resource providing information on gene expression patterns under different biological conditions in a variety of species. Gene expression data is re-analysed in-house to detect genes showing interesting baseline and dif ...

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 GenomeRNAi database collects RNAi phenotypes recorded in the literature for Homo sapiens and Drosophila melanogaster, as well as details on RNAi reagents. The data is well integrated with information from other resources, allowing comparison with ...

The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range ...

The Chemical Effects in Biological Systems (CEBS) database houses data of interest to environmental health scientists. CEBS is a public resource, and has received depositions of data from academic, industrial, and governmental laboratories.

The e-Mouse Atlas of Gene Expression (EMAGE) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descripti ...

BloodSpot is a database of mRNA expression in healthy and malignant haematopoiesis and includes data from both humans and mice. The core function of BloodSpot is to provide an expression plot of genes in healthy and cancerous haematopoietic cells at ...

Gene expression and neuroanatomical data.

Cyclebase is a database to visualize and download results from genome-wide cell-cycle-related experiments. In addition to genome annotation, Cyclebase also provides mRNA data, protein expression data, and integrated cell-cycle phenotype information f ...

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 ...

CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-datas ...

Gene Signature DataBase

ChIP-Seq, RNA-Seq and DNase-Seq data for haematopoietic and embryonic stem cells

SAGEmap provides a tool for performing statistical tests designed specifically for differential-type analyses of SAGE (Serial Analysis of Gene Expression) data. The data include SAGE libraries generated by individual labs as well as those generated b ...

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

GermOnline is a cross-species database gateway focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. The portal provides access to the Saccharomyces Genomi ...

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

Database for cross species expression pattern comparisons

Probe-Level Annotation Database for Affymetrix microarrays

ViBrism DB is a database for anatomical gene expression maps and topological co-expression network graphs created with original techniques of microtomy-based gene expression measurements, Transcriptome Tomography. The DB is equipped with a WebGL-base ...

Wiki on all aspects of next-generation genomics

Expression data to explore spatio-temporal dynamics of mitochondrial biogenesis

GEISHA (Gallus Expression In Situ Hybridization Analysis) is a centralized and comprehensive repository of precise spatial and temporal information on chicken embryonic gene expression created through in situ hybridization. Annotations include probe ...

Stemformatics is an established gene expression data portal containing over 420 public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Developed for the stem cell community, it has a major focu ...

The GENSAT (Gene Expression Nervous System ATlas) database captures information on gene expression in mouse brain at several developmental ages. The project began at Rockefeller University in New York under the direction of Nat Heintz, and has since ...

STAB is a comprehensive cell atlas resource for the human brain, containing single-cell gene expression profiling of 42 cell subtypes across 20 brain regions and 11 developmental periods. With cell subtypes and their marker genes defined by a unified ...

Cancer microarray data by gene or cancer type

Gene expression patterns in the mouse

Database of experimental results on gene expression

A database of circadian expression profiles

Weighted gene co-expression tool

Database of Gene Expression in Mouse Haematopoiesis

Many Microbe Microarrays Database

SAGE data on gene expression in male germ cell development

Sex bias in insect gene expression database

Gene co-expression data mapped to medical subject headings (MeSH).

RNAseq based human gene and transcript co-expression map

Spermatogenesis-related genes

Spatial organization of metabolic reactions in the mouse

Expression patterns in an embryonic stem library of gene trap insertions

Nottingham Arabidopsis Stock Centre microarray database

Expression and epigenetic data for mouse hematopoietic cell types

Genes transcribed in differentiating human erythroid cells

Stanford Tissue Microarray Database

Arabidopsis gene sequence tags

Public Affymetrix probesets and annotations

Yeast expression data

International mouse Gene Trap Consortium data

Gene expression data on mouse embryos

Plasma membrane protein sequences, literature, and expression database

ITTACA centralizes public datasets containing both microarray gene expression and clinical data of tumors. ITTACA currently focuses on breast carcinoma, bladder carcinoma, and uveal melanoma. A web interface allows users to carry out different class ...

The rOGED provides immediate analysis of spatio-temporal gene expression profiles for over 28,000 genes in the rat ovarian tissue during follicular growth and the preovulatory period. The database was constructed from total RNA isolated from intact o ...

The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by i ...

Current gene co-expression databases do not support cell-specific analysis because the gene expression matrices for co-expression analysis are from multiple tissues or a mix of cells and tissues. The overall correlation in gene expression identified ...

The COLOMBOS database (http://www.colombos.net) features comprehensive organism-specific cross-platform gene expression compendia of several bacterial model organisms and is supported by a fully interactive web portal and an extensive web API. COLOMB ...

ABA (Ascidian Body Atlas) is a digital 3D atlas of ascidian embryo development and gene expression pattern. Our 3D embryo images were reconstructed from more than 3,000 high-resolution real images acquired by a confocal laser microscopy in different ...

The GPX Macrophage Expression Atlas (GPX-MEA) is an online resource for expression based studies of a range of macrophage cell types following treatment with pathogens and immune modulators. GPX Macrophage Expression Atlas (GPX-MEA) follows the MIAME ...

GeneNote is a database of gene expression in normal adult human tissues, based on in-house DNA array experiments using Affymetrix GeneChip HG-U95A-E (http://www.affymetrix.com/analysis/index.affx). The goals of the project are as follows: to create ...

CAGE Basic and Analysis Databases store an original resource produced by CAGE (cap-analysis gene expression; 1), which measures expression levels of transcription starting sites (TSS) by sequencing large amounts of transcript 5'-ends, termed CAGE tag ...

The TRANSFAC® database has been constructed to model the interaction of eukaryotic transcription factors with their DNA-binding sites and how this affects gene expression. At its core are the three tables FACTOR, SITE, and GENE. A link between FACTOR ...