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Human Protein Atlas

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.

Expression Atlas

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.

Colorectal cancer atlas

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.

LoQAtE / Localizaiton and Quantitation Atlas of the yeast proteomE

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.

YPED / Yale Protein Expression Database

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.


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.

HGDP / Human Genome Diversity Project

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.

READ DB / RNA Binding Protein Expression and Disease Dynamics database

A non-redundant, curated database of human RNA binding proteins (RBPs). RBPs curated from different experimental studies are reported with their annotation, tissue-wide RNA and protein expression levels, evolutionary conservation, disease associations, protein-protein interactions, microRNA predictions, their known RNA recognition sequence motifs as well as predicted binding targets and associated functional themes, providing a one stop portal for understanding the expression, evolutionary trajectories and disease dynamics of RBPs in the context of post-transcriptional regulatory networks.


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.

MOPED / Multi-Omics Profiling Expression Database

Provides a repository for multi-omics data of human and model organisms. MOPED uses a pathway-centric view to integrate protein and gene expression data. It can assist researchers to: (1) detect potential proteins to study based on expression levels, (2) compare expression of different proteins across experiments, conditions localization and tissues, (3) search expression levels in several tissue types, cell lines, conditions and diseases and to (4) associate uncharacterized proteins to diabetes and cancer.