Determining the genes expressed for every tissue and cell type in the body has important consequences for basic cell biology, generating hypotheses for gene function and studying transcriptional changes in disease. Gene expression signatures have been used to make clinical predictions in a number of cancers and to elucidate basic gene expression biology.
Simulates Illumina reads using empirical profiles. pIRS is a simulator developed to reproduce similar to those generated from the Illumina platform. This method is helpful for developing next-generation sequencing (NGS) software such as de novo assembly, single-nucleotide polymorphism (SNP) calling and structural variation detection. This application can also be useful for applications that need heterozygous data.
Provides a bioinformatics framework to organize biology around the sequences of large genomes. Ensembl provides stable automatic annotation of genome sequences, available as either an interactive website or as flat files. It can integrates manually annotated gene structures from external sources where are available. This resource includes access to all of services and documentation, including the REST API and BioMart.
Offers an extensive and well-curated community resource of mouse developmental expression information. GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments through curation of the scientific literature and by collaborations with large-scale expression projects. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches. GXD includes over 1.5 million expression results and more than 300 000 images, all annotated with detailed and standardized metadata.
Gathers annotated sets of genes involved in biochemical pathways, signaling cascades, expression profiles from research publications, and other biological concepts. MSigDB is a database to supply gene sets for Gene Set Enrichment Analysis (GSEA). Gene sets in this repository are lists of genes (in no particular order, each gene occurs only once in the set) with annotations and links to external sources.
Permits to access, discover and disseminate omics data sets. OmicsDI is an open-source platform that can integrate proteomics, genomics, metabolomics and transcriptomics data sets. This platform stores biological and technical metadata from these public data sets using an efficient indexing system that can integrate different biological entities, including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed.
Offers annotation for over 95 000 genomes. RefSeq assigns informative names to genes, provides some annotation for every gene found in each genome it analyzes, and supports comparative studies by using consistent structural and functional annotation methods. This database uses tailored data models and processes flows to deliver reference collections for eukaryotes, viruses and prokaryotes.
Summarizes analysis-ready expression data for genes, exons, exon–exon splice junctions and base-level coverage. ReCount is an online resource that uses analysis pipelines that are annotation agnostic to process and summarize samples. The data provided allow multiple downstream analyses, including testing for differential expression of potentially unannotated transcribed sequence, enabling studies that individual laboratories would otherwise not have the resources to undertake.
Enables simultaneous comparisons between a wide range of data by combining major resources from human and vertebrate model organisms. Manteia performs several types of analyses as well as data retrieval, gene or probe set annotation, information content analysis or candidate gene prediction and prioritization. It aims to help in investigating the genetic origin of human diseases or identifying significant correlations in lists of genes and proteins generated by modern high-throughput techniques.
Provides visualization, querying tools for data mining and network exploration around Helianthus annuus. Heliagene offers a reference genome and companion resources to accelerate breeding programs. The platform focuses on the flowering time and provides precisely mapping loci that contribute to other ecologically and agriculturally important traits in wild and domesticated individuals. Tools are sorted in two categories: genomes and transcriptomes.
Provides a resource that can be utilized for clinical, genomic, transcriptomic and functional analyses of acute myeloid leukaemia (AML) biology. Vizome is an online data browser that offers expression-signature heat maps for drug. It also includes a workflow in which the data normalization, curve fit parameters and quality assurance/quality control steps are summarized.
Aims to assist scientists in infectious-disease research. PATRIC is a National Institute of Health (NIH) supported bioinformatics resource center that has been built to enable comparative genomic analysis of bacterial pathogens. The database provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Tools and services for bacterial infectious disease research are also available.
Gathers gene and protein information about for bacillus subtilis. SubtiWiki is a collective repository including data about more than 6000 protein and RNA-coding genes, over 1700 operons and links towards more than 6800 publications and 40 interactive maps of metabolic and regulatory pathways. The database displays records for individual gene and protein coupled to various modules dealing with metabolic pathways, regulation data, expression, manually curated protein-protein interaction data and genome.
Regroups in situ gene expression patterns allowing users to make queries about mouse developmental gene expression. EMAGE is an online repository that aims to describe gene expression patterns within the developing of mouse embryo and that includes: spatially mapped patterns of messenger RNA (mRNA), in situ hybridization (ISH), protein immunohistochemistry (IHC) and transgenic reporter data.
A literature-based gene resource for exploring epithelial-mesenchymal transition (EMT)-related human genes. dbEMT includes literature data, clinical relevant variants, gene expression profiles and biological pathways. It is constructed as a free database and analysis server to enable users to rapidly search and retrieve summarized EMT-related genes.
Contains image and phenotype data for embryonic lethal knockout mice. DMDD is database allowing to search by gene, phenotype or tissue type. The data sheds new light on genes that are critical for embryo development and survival. High-resolution 3D image analysis and tissue histology are used to identify abnormalities in both embryos and placentas from embryonic lethal lines. It provides Full-resolution images, phenotypes annotated on the relevant images and Phenotype penetrance data for each line. The database also includes gene expression profiles for embryos from knockout lines.
Provides a collection of single-cell transcriptomic profiles from mouse tissues, organs, and cell cultures. MCA furnishes information of over 800 major cell types and potentially more than 1 000 cell subtypes in the mouse system. It allows public discussion, correction, and validation of annotated cell types. This database can serve to discover uncharacterized cross-tissue cellular hierarchy.
Captures the mean expression patterns of many genes in a common frame despite significant variations in morphology and expression between individual embryos. VirtualEmbryo is a database that contains data for 95 genes at six time cohorts for Drosophila Melanogaster. This online resource also provides a comprehensive visualization tool for examining relationships between different gene expression patterns.
A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. BCaPE provides tools for visualizing, querying and downloading data from a large collection of highly molecularly annotated breast cancer patient-derived tumour xenografts (PDTX). The biobank represents a powerful resource for pre-clinical breast cancer pharmacogenomic studies, including identification of biomarkers of response or resistance.
Consists of a community resource dedicated to the study of parasitic nematodes. Nematode.net provides access to annotation of genomes, expression and related genome-scale data, as well as data-mining tools and their comparative data products. It hosts annotation for more than 1 million genes and transcripts. It includes a module, NemaBrowse, that allows the displaying of SnpEff-annotated variants from isolates with different phenotypes. The database is a part of Helminth.net, an evolving collection of databases hosting resources for helminths.