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Signaling pathway crosstalk databases | Protein interaction analysis

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Offers a way to search and discover the relationships among genes, proteins, compounds and small RNAs in plant signal transduction, metabolism and gene regulatory networks. HRGRN models the interactions between nodes by defining comprehensive types of edges. It provides connection by edges between the genes with similar expression patterns, which will provide in-depth insight into gene–gene relationships. The database permits to discover novel interactions between genes and/or pathways and the built-in analysis tool available on the site allows to build subnetworks for specified nodes based on known interactions.
An integrated database resource consisting of 16 main databases, which are categorized into systems, genomic, chemical and health information. The PATHWAY, BRITE and MODULE databases in the systems information category contain KEGG pathway maps, BRITE hierarchy and table files and KEGG modules, respectively, as representations of high-level functions. They are all manually created based on published literature. The genomic information category contains the GENOME and GENES databases for collections of organisms with complete genomes and their gene catalogs, which are mostly taken from RefSeq and GenBank databases. The COMPOUND, GLYCAN, REACTION, RPAIR, RCLASS and ENZYME databases in the chemical information category contain chemical substances and reactions and are collectively called KEGG LIGAND for historical reasons. The health information category consists of the DISEASE, DRUG, DGROUP and ENVIRON databases for disease and drug information.
An integrated resource to analyze signaling pathway cross-talks, miRNAs and regulatory enzymes in zebrafish. SignaFish contains more than 200 curation-based signaling interactions, 132 further interactions listed in other resources, and it also lists potential miRNA-based regulatory connections for seven major signaling pathways. From the SignaFish website, users can reach other web resources, such as ZFIN. SignaFish provides signaling or signaling-related interactions that can be examined for each gene or downloaded for each signaling pathway. SignaFish serves as a navigating point for experimental design and evaluation for the zebrafish community and for researchers focusing on nonmodel fish species, such as cyclids.
SIGNOR / SIGnaling Network Open Resource
Organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The entire network can be freely downloaded and used to support logic modeling or to interpret high content datasets. The core of this project is a collection of more than 11000 manually-annotated causal relationships between proteins that participate in signal transduction. Each relationship is linked to the literature reporting the experimental evidence. In addition each node is annotated with the chemical inhibitors that modulate its activity. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.
Aging Chart
A wiki-based visual encyclopedia of aging processes that will facilitate rapid exploration of aging pathways and mechanisms by experts and entrants to the field alike. Building on an initial content base constructed by a team of experts from peer-reviewed literature, users can integrate new data into biological pathway diagrams for a visible, intuitive, top-down framework of aging processes that fosters knowledge-building and collaboration. Aging Chart is an extension of the community curation model for pathway collections and is the first such resource to serve the growing community of researchers interested in the cellular and molecular biology of aging.
pathDIP / pathway Data Integration Portal
An annotated database of signaling cascades. PathDIP integrates data from 20 source pathway databases, comprising core pathways from major curated pathways databases, and extended pathways predicted by using physical protein interactions. Data integration and predictions increase coverage of pathway annotations for protein-coding genes to 86%, and provide novel annotations for 5,732 pathway orphans. PathDIP annotates 17,070 protein-coding genes with 4,678 pathways, and provides multiple query, analysis and output options.
A comprehensive database resource for systems biology of DNA damage and repair. REPAIRtoire collects and organizes the following types of information: (i) DNA damage linked to environmental mutagenic and cytotoxic agents, (ii) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, (iii) proteins participating in DNA repair and (iv) diseases correlated with mutations in genes encoding DNA repair proteins. Pathways are represented as graphs and in tabular form with descriptions of each repair step and corresponding proteins, and individual entries are cross-referenced to supporting literature and primary databases. REPAIRtoire can be queried by the name of pathway, protein, enzymatic complex, damage and disease.
A database of signaling pathway crosstalk. XTALKDB contains curated information for 650 pairs of pathways from over 1,600 publications. In addition, the database reports the molecular components (e.g. proteins, hormones, microRNAs) that mediate crosstalk between a pair of pathways and the species and tissue in which the crosstalk was observed. The XTALKDB website provides an easy-to-use interface for scientists to browse crosstalk information by querying one or more pathways or molecules of interest.
ACSN / Atlas of Cancer Signalling Network
Describes in detail signalling and regulatory molecular processes that occur in a healthy mammalian cell. ACSN is characterized by several features: (i) it is a comprehensive description of cancer related mechanisms retrieved from the most recent literature, (ii) its content is represented as an interactive global map that can be browsed with Google Maps interface, (iii) it has an online discussion forum, allowing users to provide feedback and (iv) it has a built-in tool box for visualization and analysis of high-throughput data in the context of the comprehensive signalling network.
Provides an Alzheimer’s disease (AD) intra, inter and extra cellular pathway map curated from scientific literature. AlzPathway is a platform with the aim of enabling the evaluation of candidate risk genes listed by genome wide association studies (GWAS) and the analysis of omics data to reveal pathogenesis of AD. It includes more than 30 canonical pathways encompassing about 1300 species, 1000 reactions and more. The repository is available as both a web application and a SBML file that can be read by CellDesigner.
ScaPD / Scaffold Protein Database
Provides an information’s repository for scaffold proteins and associated signaling pathways. ScaPD contains more than 270 scaffold proteins and over 1100 distinct scaffold-mediated phosphorylation pathways. The database is manually curated from, in part, Google Scholar and PubMed literature and, in other part, from a bioinformatic approach for detecting scaffold proteins. Users can download predicted or experimental datasets or browse a specific search.
DDRprot / DNA Damage Response proteins
Integrates manually curated information on the human DNA damage response network and its sub-pathways. DDRprot is presented within an evolutionary framework that allows many features to be explored and as such, we believe it will be very useful to researchers in the field. DDRprot database can be queried by different criteria: pathways, species, evolutionary age or post-translational modifications. Sequence searches using hidden Markov models can be also used.
MirOB / MicroRNA OncoBase
MicroRNA targets database and data analysis and visualization tool. An integrative instrument for dissecting complex role microRNA in cancer. The Database includes more than 8500 manually curated interactions represented the main human intracellular pathways. A large proportion of the interaction set involved into microRNAs and Transcription Factors Targets networks. A special attention is paid to specific types of human cancers, pathological processes and expression level alterations in cancers.
An integrated dataset of human pathways and protein-protein interactions. We developed a series of rules for transforming protein interactions from pathway to binary model, and the protein interactions from seven pathway databases, including PID, BioCarta, Reactome, NetPath, INOH, SPIKE and KEGG, were transformed based on these rules. These pathway-derived binary protein interactions were integrated with PPIs from other five PPI databases including HPRD, IntAct, BioGRID, MINT and DIP.
INOH / Integrating Network Objects with Hierarchies
A highly structured, manually curated database of signal transduction pathways including Mammalia, Xenopus laevis, Drosophila melanogaster, Caenorhabditis elegans and canonical. Since most pathway knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form. We use a hierarchical pathway representation model with a compound graph, and every pathway component in the INOH database is annotated by a set of uniquely developed ontologies. Finally, we developed the Similarity Search using the combination of a compound graph and hierarchical ontologies. The INOH database is to be a good resource for many users who want to analyze a large protein network. INOH ontologies and 73 signal transduction and 29 metabolic pathway diagrams (including over 6155 interactions and 3395 protein entities) are freely available in INOH XML and BioPAX formats.
HSPD / Hedgehog Signaling Pathway Database
A curated repository of information pertaining to the Hedgehog developmental pathway. The Hedgehog Signaling Pathway Database is designed to provide centralized access to a wide range of relevant information in an organism-agnostic manner. Data are provided for all genes and gene targets known to be involved in the Hh pathway across various organisms. The data provided include DNA and protein sequences as well as domain structure motifs. All known human diseases associated with the Hh pathway are indexed including experimental data on therapeutic agents and their molecular targets.
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