ChIPBase, an integrated resource and platform for decoding transcription factor binding maps, expression profiles and transcriptional regulation of long non-coding RNAs (lncRNAs, lincRNAs), microRNAs, other ncRNAs(snoRNAs, tRNAs, snRNAs, etc.) and protein-coding genes from ChIP-Seq data. ChIPBase currently includes millions of transcription factor binding sites (TFBSs) among 6 species. ChIPBase provides several web-based tools and browsers to explore TF-lncRNA, TF-miRNA, TF-mRNA, TF-ncRNA and TF-miRNA-mRNA regulatory networks. ... [Information of the supplier]
dbVar is a database of genomic structural variation that allows you to search, view, and download variant data from studies submitted for any organism. In general, variants are ≥ 50 nucleotides, but are occasionally smaller. dbVar provides access to the raw data (when available) and links to other NCBI and external resources. ... [Information of the supplier]
The Death domain (DD) superfamily is one of the largest classes of protein interaction modules and plays a pivotal role in the apoptosis, inflammation, necrosis, and immune cell signaling pathways. Critical caspase activating complexes in the apoptosis and inflammation signaling pathways are assembled via the DD superfamily. These domains are also involved in recruiting downstream effectors for immune cell receptor signaling, intracellular pathogen sensing, and response to DNA damage. To stimulate future researches among scientists who are interested in the DD superfamily mediated signaling pathway, we have developed the Death Domain Database, a manually curated database that aims to provide comprehensive information on PPIs of human DD superfamily. The current version of the Death Domain Database documents 175 PPI pairs among 99 DDS by curating 295 peer-reviewed publications. The Death Domain Database provides a detailed summary of PPI data, which fits into 3 categories: interaction, characterization, and functional role. Users can find in-depth information specified in the literature on relevant analytical methods, structural information. The Death Domain Database has a user-friendly interface with several helpful features, including a search engine, an interaction map, and a function for cross-referencing useful external databases. Our Death Domain Database will provide a valuable tool to assist in understanding and organizing the molecular interaction network of the DD superfamily. ... [Information of the supplier]
The Database of Genomic Variants archive (DGVa) is a repository that provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. In recent years there have been unprecedented advances in the technologies that characterise genomic variation, and it is well known that variation at the single nucleotide level is abundant across the genomes of all species. However, it is becoming clear that genomic structural variation - this is variation ranging from tens to millions of base pairs in size and includes insertions, deletions, inversions, translocations and locus copy number changes - accounts for more of the individual differences at the base pair level in humans and is likely to play a major role in disease. Two other areas of research that are becoming increasingly important in this field are discovering how genomic structural variation affects an individual's characteristics, and understanding the role it has played in the evolution of species. The DGVa catalogues, stores and freely disseminates this important class of variation in any species, providing a valuable resource to a large community of researchers. ... [Information of the supplier]
The DistiLD database aims to increase the usage of existing genome-wide association studies (GWAS) results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context. The database performs three important tasks: 1. published GWAS are collected from several sources and linked to standardized, international disease codes ICD10 codes) 2. data from the International HapMap Project are analyzed to define linkage disequilibrium (LD) blocks onto which SNPs and genes are mapped 3. the web interface makes it easy to query and visualize disease-associated SNPs and genes within LD blocks. ... [Information of the supplier]
DNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study: Homo sapiens (human), Mus musculus (mouse), Drosophila melanogaster (fruit fly), Caenorhabditis elegans (nematode), Saccharomyces cerevisiae (budding yeast), Schizosaccharomyces pombe (fission yeast), Escherichia coli K-12, Arabidopsis thaliana (mouse-ear cress) DNAtraffic contains comprehensive information on diseases related to the assembled human proteins. Database is richly annotated in the systemic information on the nomenclature, chemistry and structure of the DNA damage and drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA metabolism pathway analysis. Database includes illustrations of pathway, damage, protein and drug. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines it has to be extensively linked to numerous external data sources. Database represents the result of the manual annotation work aimed at making the DNAtraffic database much more useful for a wide range of systems biology applications. DNAtraffic database is freely available and can be queried by the name of DNA network process, DNA damage, protein, disease, and drug. ... [Information of the supplier]
No other database than ESTHER holds all alpha/beta hydrolase fold proteins together: Interpro, Prosite, Pfam, have multiple entries for subsets of this structural superfamily. A table Synthese shows the correspondance between these database entries and the subfamilies in ESTHER. The ESTHER Table is now a little to big to be usefull. Each file contains one of the 31219 non redundant proteins/genes. The tables grouped in the family table, the syntheses table or the structure table may be more usefull. The Gene_locus nomenclature for these non-redundant entries is a name with 5 characters for the organisms (3 for genera, 2 for the species, except when a common 5 character name exists. ex: ratno is for Rattus norvegicus and human for man. This allows us to keep close to the Swiss-Prot nomenclature). The last characters define the protein, ex: human-acche represents human acetylcholinesterase. ... [Information of the supplier]
The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our partners in the International Nucleotide Sequence Database Collaboration (INSDC). ENA is made up of a number of distinct databases that includes EMBL-Bank, the newly established Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. ... [Information of the supplier]
The Encyclopedia of DNA Elements (ENCODE) consortium aims to identify all functional elements in the human genome sequence. These elements include genomic regions bound by transcription factors (TFs), occupied by nucleosomes, occupied by nucleosomes with modified histones, hypersensitive to cleavage of DNase I, etc. We organize the on-going analysis results of TF binding data in the web accessible repository factorbook.org. ... [Information of the supplier]
hiPathDB provides two different types of integration. The pathway-level integration is a simple collection of individual pathways as described in the original database. We devised a gene-centric pathway model that could reflect different properties of four databases. The entity-level integration creates a super pathway that merged all pathways by unifying redundant components. Even though the detailed molecular information such as complex formation or modification can be lost in some cases, the merged superpathway provides a unified view of current knowledge on human pathways, which is critical to understand relationships among different pathways. Another strong merit of hiPathDB is the built-in pathway visualization module to support explorative study of complex networks in an interactive fashion. The force-directed layout algorithm is optimized for almost automatic visualization of pathways. ... [Information of the supplier]
