Gathers information about the protein-coding genes of seventeen major cancer types and their genome-wide transcriptome. Pathology Atlas is an open-access database, part of the Human Protein Atlas, which aims to examine the prognostic role of each protein-coding gene in the different cancers. The database uses transcriptomics and antibody-based profiling to provide a standalone resource for cancer precision medicine.
A knowledge-based portal with gene-centric expression profiles based on the annotation of several antibodies towards the same protein target. Because all the data on the Human Protein Atlas are publicly available, the information can be integrated into other databases. The availability of the annotated expression patterns opens up the possibility for a community-based dialog to provide input by researchers with specialized knowledge about particular protein targets.
Provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. Expression Atlas consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Expression Atlas search interface allows for querying one or more genes or proteins from a selected species. The user can also add search filters for sample attributes and experimental factors, taking full advantage of ontology-driven query expansion.
Provides multi-omic data about inflammatory bowel disease (IBD). IBDMDB considers the gut microbial ecosystem as a target for diagnosis, therapy, and mechanistic understanding of IBD. It can be used to estimate if microbial composition predicts subsequent risk of flares in disease activity. This platform is useful for determining the response to a given therapy using the stool microbiota.
Consists of a cell type- and brain region-specific atlas of open chromatin. BOCA assists users in the investigation of the regulation of gene expression in the brain. It can serve for the study of the impact of neuropsychiatric disease risk variants. This tool furnishes maps of neuronal and non-neuronal chromatin accessibility across 14 distinct brain regions of 5 adult individuals.
An integrated web-based resource that catalogues the genomic and proteomic annotations identified in colorectal cancer (CRC) tissues and cell lines. The data catalogued to-date include sequence variations as well as quantitative and non-quantitative protein expression data. The database enables the analysis of these data in the context of signaling pathways, protein–protein interactions, Gene Ontology terms, protein domains and post-translational modifications. Currently, Colorectal Cancer Atlas contains data for >13 711 CRC tissues, >165 CRC cell lines, 62 251 protein identifications, >8.3 million MS/MS spectra, >18 410 genes with sequence variations (404 278 entries) and 351 pathways with sequence variants. Overall, Colorectal Cancer Atlas has been designed to serve as a central resource to facilitate research in CRC.
Contains easily accessible and user-friendly information about subcellular localization and levels for 5330 yeast proteins under three environmental stress conditions and two genetic perturbations. Using LoQAtE DB, users can get a profile of changes for proteins of interest as well as querying advanced intersections by either abundance changes, primary localization or localization shifts over the tested conditions. Currently, the DB hosts information on 5330 yeast proteins under three external perturbations (DTT, H2O2 and nitrogen starvation) and two genetic mutations [in the chaperonin containing TCP1 (CCT) complex and in the proteasome]. Additional conditions will be uploaded regularly. The data demonstrate hundreds of localization and abundance changes, many of which were not detected at the level of mRNA. LoQAtE is designed to allow easy navigation for non-experts in high-content microscopy and data are available for download.
Provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. PSI-MR is a resource that informs about plasmids, theses plasmids permits researchers to find the biological function of protein. For each PSI plasmid, user can retrieve additional resources simplifying cross-referencing of a particular plasmid to protein annotations and experimental data.
An online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections. MyMpn hosts a wealth of omics-scale datasets generated by hundreds of experimental and computational analyses. These include data obtained from gene expression profiling experiments, gene essentiality studies, protein abundance profiling, protein complex analysis, metabolic reactions and network modeling, cell growth experiments, comparative genomics and 3D tomography.
Provides information about human cells. SHOGoiN Cell Database contains cell differentiation pathways compiled from biomedical textbooks and journal papers and includes its own cell classification scheme in which each human cell is classified according to physical locations. Several cell taxonomy keys exist to tidy human differentiated cells and stem cells.
Contains gene-tissue associations in human and three mammalian model organisms. TISSUES provides tissue associations protein-coding genes, collected from multiple sources and data types. It includes confidence scores for every associations to make them comparable across data sources, data types, and organisms. This database shows gene-tissue correlations between orthologous and paralogous genes, simplifying comparisons across organisms.
Allows to genetic diversity in human populations. HGDP has collected genomic DNA from 1,043 individuals from around the world and has determined their genotypes at more than 650,000 single nucleotide polymorphism (SNP) loci. It represents 51 different populations from Africa, Europe, the Middle East, South and Central Asia, East Asia, Oceania and the Americas. The database shares ancestry and admixture, relationships between haplotype heterozygosity and geography, and population differences in copy number variation (CNV) throughout the human genome in the 1,043 individuals.
Provides mutations on the genomic, RNA, and protein level. KinMutBase is an online resource that contains information on occurrences of mutations such as the number of patients, number of unrelated families, and the number of patients homozygous for a mutation. In addition to mutations, this database also includes several other types of information.
Allows users to store, retrieve, and perform integrated analysis of data from high throughput proteomic technologies. YPED is a web-accessible database for managing, querying, viewing, interpreting, and archiving data derived from multiple, state of-the-art protein profiling technologies. It consists of three components: an Oracle database server, a web interface and an ftp file server. The database is designed to capture DIGE data in addition to data generated by other protein profiling techniques including MudPIT, ICAT, and iTRAQ.
Gathers data dealing with protein microarrays. PMD consists of a repository of information curated from the GEO/ArrayExpress databases, scientific literatures, as well as user’s contributions. This database is divided into four sections supplying information about: (i) raw data and samples annotation, (ii) array platforms, (iii) scientific publications related to microarray as well as (iv) a set of tools for data analysis.
Provides easy and intuitive access to protein synthesis data derived from various proteomics experiments. Aureolib is by far the most comprehensive protein expression database for S. aureus and provides an essential tool to decipher more complex adaptation processes in S. aureus during host pathogen interaction.
A model of the molecular networks present in grapevines. VitisNet allows visualization of the dynamic interactions in the transcriptome, proteome, and metabolome within known molecular networks (for example, metabolic or signaling pathways). Integrating transcripts with protein and metabolite profiles in a comprehensive molecular map enables the researcher to elucidate different biochemical responses of grapevines to developmental and environmental cues. VitisNet uses manually annotated networks in SBML or XML format, enabling the integration of large datasets, streamlining biological functional processing, and improving the understanding of dynamic processes in systems biology experiments.
A large database resource and suite of data visualization tools designed to interrogate how the abundance of proteins and their isoforms change as a function of developmental stage in Caenorhabditis elegans. All the raw data used to develop this resource are available for download.
Stores Varroa destructor life cycle proteins. Varroa protein atlas cross all major developmental stages (egg, protonymph, deutonymph and adult) for both male and female mites as a web-based interactive tool. The atlas was built using the framework for the honey bee protein atlas. It features a searchable database of the quantified proteins as well as a visual and numerical display of their relative expression in different developmental stages.