Tag: molecular interactions, pathways and networks

Medical Subject Headings is the National Library of Medicine - controlled vocabulary used for indexing articles for PubMed and other NLM databases.

REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database.

The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications.

The information in the database is presented at two levels: the initial view or landing pages for each target family provide expert-curated overviews of the key properties and selective ligands and tool compounds available. For selected targets more ...

Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...

MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. MINT ...

WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.

DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific liter ...

The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored w ...

The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. Releases: https://githu ...

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts publish ...

The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relations ...

Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for ide ...

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in ...

BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-link ...

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez can effic ...

Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.

GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes.

MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecu ...

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely av ...

The Rat Genome Database stores genetic, genomic, phenotype, and disease data generated from rat research. It provides access to corresponding data for eight other species, allowing cross-species comparison. Data curation is performed both manually an ...

Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis which was created to improve knowledge of developmental and disease processes. Through curation and automated data provisioning from various sources, Xenbase aims ...

DIANA-TarBase is a reference database that indexes experimentally-supported microRNA (miRNA) targets. It integrates information on cell-type specific miRNA–gene regulation and includes miRNA-binding locations. The target data provided by DIANA-TarBas ...

STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-ca ...

BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs.

The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, ...

VirHostNet 2.0 integrates an extensive and original literature-curated dataset of virus/virus and virus/host protein-protein interactions complemented with publicly available data.

EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc ha ...

The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant.

MODOMICS is the first comprehensive database system for biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that ...

Drug-related information: medical indications, adverse drug effects, drug metabolism and Gene Ontology terms of the target proteins.

The I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs). It has been built by mapping high-throughput (HTP) data between species.

DBETH is the Database of Bacterial Exotoxins for Human. The aim of this database is to assemble information on the toxins responsible for causing bacterial pathogenesis in humans.

The SIGnaling Network Open Resource. The core of SIGNOR is a collection of approximately 12,000 manually-annotated causal relationships between over 2800 human proteins participating in signal transduction. Other entities annotated in SIGNOR are comp ...

As a database, miRTarBase has accumulated more than fifty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to fu ...

MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondin ...

This database enables the reliable identification of an individual Interferon Regulated Gene (IRG) or IRG signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It also assists in identifying regulatory elements, chromosoma ...

YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 ...

Overview The NIH Mammalian Gene Collection (MGC) program is a multi-institutional effort to identify and sequence cDNA clones containing a full-length open reading frame (FL-ORF) for human, mouse, and rat genes. To date, the MGC has produced over 324 ...

The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. The resource provides categorical information ...

RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell. On the other hand, it is also a model of the organization of the genes in transcription units, operons and simple and complex regulons. In t ...

The GeneWeaver data and analytics website is a publically available resource for storing, curating and analyzing sets of genes from heterogeneous data sources. The system enables discovery of relationships among genes, variants, traits, drugs, enviro ...

H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splici ...

Phospho.ELM is a manually curated database of eukaryotic phosphorylation sites. The resource includes data collected from published literature as well as high-throughput data sets.

The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology term ...

MetaNetX/MNXref is a database for reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. The tools developed at MetaNetX are useful for accessing, analysing and manipulating metabolic networks. Meta ...

Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and beneficial interactions. The updated Microbial Signal Transduct ...

The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details neces ...

SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.

Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization, and management. It integrates protein-protein interaction (PPI) data from public curated ...

Kinase-Ligand Interaction Fingerprints and Structures database (KLIFS) is a database that revolves around the protein structure of catalytic kinase domains and the way kinase inhibitors can interact with them. Based on the underlying systematic and c ...

iPAVS provides a collection of highly-structured manually curated human pathway data, it also integrates biological pathway information from several public databases and provides several tools to manipulate, filter, browse, search, analyze, visualize ...

The Legume Information System (LIS) is a collaborative, community resource to facilitate crop improvement by integrating genetic, genomic, and trait data across legume species.

microRNA-mRNA interaction maps

Zfishbook is a real-time database of transposon-labeled mutants in zebrafish. This resource provides services for any size of GBT mutagenesis projects on zebrafish to encourage collaboration in the research community.

Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.

The BioCyc collection of Pathway/Genome Databases (PGDBs) provides electronic reference sources on the pathways and genomes of hundreds of organisms with completely sequenced genomes. Each database contains the genome, predicted metabolic pathways, p ...

Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web-based tools for sequence analysis (i.e. Blast, Motif, Clustal W).

GWASdb comprises of collections of traits/diseases associated SNP (TASs) from current GWAS and their comprehensive functional annotations, as well as disease classifications.

Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.

A suite of Web-based tools for comparative genomics

The Arabidopsis Gene Regulatory Information Server (AGRIS) is a new information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains two databases, AtcisDB (Arabidopsis thaliana cis-regula ...

CellPhoneDB is a publicly available repository of curated receptors, ligands and their interactions. Subunit architecture is included for both ligands and receptors, representing heteromeric complexes accurately. This is crucial, as cell-cell communi ...

FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain. The FlyCircuit Database currently contains about 30,000 high resolution 3D br ...

The Network of Cancer Genes (NCG) contains information on duplicability, evolution, protein-protein and microRNA-gene interaction, function, expression and essentiality of cancer genes from manually curated publications . NCG also provides informatio ...

The Plant Transcription Factor Database is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and anno ...

DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 197,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure I ...

SPIKE (Signaling Pathway Integrated Knowledge Engine) is an interactive software environment that graphically displays biological signaling networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA mi ...

Corynebacterial Regulation Network a reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks.

PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other path ...

Autism genetics KnowledgeBase, an evidence-based knowledgebase of autism genetics.

The Pocketome is an encyclopedia of conformational ensembles of druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry describes a site on a protein surface that is invo ...

Collaborative resource for the Bacillus community.

Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.

Manually annotated component of UniProtKB (produced by the UniProt consortium). It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis.

A major part of this information gets extracted by manual annotation from the yeast literature, and results of the systematic functional analysis projects as well as cross-references to other in-house or external databases (NCBI, PIR, PEDANT, EMBL) p ...

Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight.

The Tomato Functional Genomics Database integrates several prior databases including the Tomato Expression Database and Tomato Metabolite Database, and the Tomato Small RNA Database.

Predicted regulons in prokaryotic genomes

BacMap is a picture atlas of annotated bacterial genomes. It is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.

Nematode.net is the home page of the parasitic nematode EST project at The Genome Institute at Washington University in St. Louis. The site was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum ...

Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.

DroID, the Drosophila Interactions Database, assembles gene and protein interaction data from a variety of sources into one easily accessible, comprehensive database. The database includes published and unpublished low and high throughput data sets, ...

The Leaf Senescence Database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. LSD includes data types such as leaf senescence-associated transcriptomics, phenotype and interaction data.

Families of nuclear hormone receptors

Cytochrome P450 alleles and drug interactions

SwissLipids is an expert-curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models. SwissLipids is updated daily.

Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.

ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accu ...

The MetaCrop resource contains information on the major metabolic pathways mainly in crops of agricultural and economic importance. The database includes manually curated information on reactions and the kinetic data associated with these reactions. ...

Known and predicted protein domain interactions observed in PDB entries,

Protein-protein and drug-protein interactions for studies of drug repositioning

Cervical cancer gene database

ADPriboDB is a database of ADP-ribosylated proteins and their literature-identified ADP-ribosylated residues. The database includes a variety of information for each entry, including any drug treatments performed to obtain the identification of the m ...

This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the EAWAG-BBD is to provide information on microbial enzyme-catalyzed reactions that are impo ...

The Prokaryotic Operon DataBase constitutes one of the most precise and complete repositories of operon predictions now available. Using our novel and highly accurate operon identification algorithm, we have predicted the operon structures of more th ...

This tool is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. The system also simplifies cross-databas ...

Inferred Biomolecular Interaction Server: protein-protein, ligand- and nucleic acid-binding sites

Data Repository for Yeast Genetic Interaction Networks

MEM (Multi-Experiment Matrix) provides gene expression similarity searches, visualisation and analyses across many datasets from ArrayExpress and GEO. MEM uses rank aggregation to merge information from different datasets into a single global orderin ...

WebGesTer Database (DB) is the largest compilation of intrinsic terminators of transcription. It comprises of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. The database is the storehouse for algorithm ...

Coexpressed genes and networks in human and mouse

Gene regulation in bacteriophages

A database of non-interacting proteins

Protein Common Interface Database

Quality assessed protein-protein interactions in 9 species

Coronary Artery Disease gene database

DISNOR is a resource that uses a comprehensive collection of disease associated genes, as annotated in DisGeNET, to interrogate SIGNOR (https://signor.uniroma2.it) in order to assemble disease-specific logic networks linking disease associated genes ...

Death Domain Database is a manually curated database of protein-protein interactions for Death Domain Superfamily.

A non-redundant database of protein-peptide complexes

Dictionary on miRNAs and their putative target pathways

Regulatory Network in Protein Phosphorylation

CyanoBase is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and m ...

CoVex is an interactive online platform for SARS-CoV-2 host interactome exploration and drug (target) identification. CoVex integrates virus-human protein interactions, human protein-protein interactions, and drug-target interactions. It allows visua ...

Cancer-relevant proteins and compound interactions

The UCSC Cancer Genomics Browser is a web-based tool to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of experimental measurements for multiple samples, alongside their associated clinical ...

Database for Human Transcription Co-Factors

Predicted Arabidopsis Interactome Resource

Prokaryotic 2-Component Systems database

Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including au ...

Database of Chromosomal Rearrangements In Diseases

DNA repair pathways of human, yeast and E.coli

The datasets list genes, environmental risk factors and autoantibodies in a number of polygenic diseases and provide KEGG pathway analysis etched out by susceptibility genes. Host/pathogen interactions are also characterised for herpes simplex, helic ...

Kazusa Plant Pathway Viewer

A database of curated biomolecular interactions.

Domain interaction map: experimental and predicted protein domain interactions

IsoRank PPI Network Alignment Based Ortholog Database

Plant metabolic, regulatory and signaling pathways

Mouse Multiple Tissue Metabolomics Database

Human Integrated Pathway Database (hiPathDB) provides two different types of integration. The pathway-level integration is a simple collection of individual pathways as described in the original database. The entity-level integration creates a super ...

An integrated database of ncRNA interactions. Noncoding RNAs (ncRNAs) play crucial regulatory roles in a variety of biological circuits. To document regulatory interactions between ncRNAs and biomolecules, we previously created the NPInter database ...

Arabidopsis thaliana Protein Interactome Database

Database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions.

Gene Ontology-based functional similarity values for proteins and protein families

Genome-WIde Docking Database: 3D structures of protein complexes

Comparison system for cancer stem cell analysis

Transcription factors (TFs) and their target genes have important functions in human diseases and biological processes. Gene expression profile analysis before and after knockdown or knockout is one of the most important strategies for obtaining targ ...

Reference database and prediction tool for the identification of cryptic recombination signal sequences (RSSs) in the human and mouse genomes.

Linking RNA splicing and disease. Database that collects and curates data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent func ...

Contains high- and low-throughput data relevant to phosphorylation events. It includes 6,225 low-throughput and 21,990 high-throughput interactions, from greater than 35,000 experiments.

Protein-protein interactions for mammalian TRP channels

Psychiatric disorders and Genes association NETwork. Exploratory analysis of psychiatric diseases and their associated genes.

Dragon Database of Genes Implicated in Prostate Cancer is a knowledgebase of genes experimentally verified to be involved in prostate cancer (PC). DDPC provides gene-associated data such as protein annotation, molecular pathways, ontologies and trans ...

Database for integration of human functional interactions

A database for systems biology of DNA dynamics during the cell life.

miRGator is an integrated database of microRNA (miRNA)-associated gene expression, target prediction, disease association and genomic annotation for the functional investigation of miRNA. miRGator v2.0 contains information about : 1) Human miRNA expr ...

Database of MacroMolecular INteractions

An acronym for the project "A pipeline for the discovery, sustainable production and commercial utilisation of known and novel high-value triterpenes with new or superior biological activities”. This is an EU-funded collaborative project on establish ...

The Gemina system (http://gemina.igs.umaryland.edu) identifies, standardizes and integrates the outbreak metadata for the breadth of NIAID category A–C viral and bacterial pathogens (http://www3.niaid.nih.gov/biodefense/PDF/cat.pdf), thereby p ...

A medical genetics information resource developed for physicians, other healthcare providers, and researchers, available at no cost to all interested persons.

Comprehensive database of fragments linking metabolites, toxic molecules and drugs

EXPath is a database resource that collects and utilizes expression profiles derived from microarray under various conditions to infer metabolic pathways for six model plants: Arabidopsis thaliana, Oryza sativa, Zea mays, Solanum lycopersicum, Glycin ...

Crosstalk among signaling pathways

TF-target relationsips inferred from single cell and bulk RNA-seq datasets

Interacting and non-interacting protein pairs

Visualize the natural connections between DNA sequences, natural variation (polymorphisms), molecular structures, protein-protein interactions, and gene expression patterns by combining several data visualization tools with a zoomable user interface.

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator cu ...

Protein–RNA interaction predictions for model organisms with supporting experimental data, enabling a global view of the protein–RNA interactome. RNAct currently covers the human, mouse and yeast genomes and contains a total of 5.87 billion pairwise ...

Comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae.

dbPSP (database of Phosphorylation Sites in Prokaryotes) is an updated resource for annotating protein phosphorylation sites (p-sites) in prokaryotes (bacteria and archaea).

RetroRules is a database of reaction rules for metabolic pathway discovery and metabolic engineering. RetroRules provides a complete set of reaction rules, extracted from public databases and expressed in the community-standard SMARTS format, augment ...

The Agronomic Linked Data (AgroLD) is a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, which integrates data about plant species of high interest for the plant science community. AgroLD is an RD ...

The Canadian Rare Diseases Models and Mechanisms (RDMM) Network. Japanese Rare Disease Models & Mechanisms Network.

OmicsDB offers an integrated platform for studying biological networks in multiple organisms, as well as accessing gene expression data. By expanding the classic single species databases across species, it is possible to leverage the amount of inform ...

Binary SubComplexes in Proteins Database

Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism and roots | A platform dedicated to the visualization and analysis of plant co-expression and co-function networks

PlantCircNet is a database that provides plant circRNA-miRNA-gene regulatory networks, as well as circRNA information and circRNA expression profiles. It provides convenient search functions for circRNA-associated regulatory networks and enables user ...

A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. AppleMDO is a multi-dimensional omics database. Users can submit locus IDs to quickly search for co-expression networks, functional modules, chromatin states a ...

Breast cancer gene-expression miner (bc-GenExMiner) 4.5 is a mining module computes breast cancer differential gene expression analyses. It is a statistical mining tool of published annotated breast cancer transcriptomic data (DNA microarrays and RNA ...

A system of databases documenting the influence of mutations in regulatory gene regions.

Information retrieval tool for accessing and integrating genetic and medical information for health applications. Resorting to this integrated environment, clinicians are able to access and relate diseases data already available in the Internet, scat ...

ARGminer is a web platform dedicated to the validation of ARGs by using sequence alignment and evidence from multiple sources.

CHG is a systematically integrated database of cancer hallmark genes. The database focuses on integrating hallmark genes in a systematic, standard way and annotates the potential roles of the hallmark genes in cancer processes.

A human immunosuppression gene database. HisgAtlas is the first database that stores a list of immunosuppression genes collected by literature mining and manual curation. 995 human immunosuppression genes and 260 associated diseases are collected in ...

Interpreting Genetic Variation in Human and Cancer Genomes Using Post-translational Modification Sites and Signaling Networks (2021 Update). Find your mutation or gene of interest. You are viewing an updated version (2021) of the ActiveDriverDB. To ...

Arabidopsis thaliana Multi-omics Association Database

Animal Social Networks Repository - repository of interaction data from published studies of wild, captive, and domesticated animals.

a tool for analyzing putative transcription factor binding sites in salmonid genomes | SalMotifDB: cis-regulatory motif database for salmonids | We're getting there, it's worth the wait

An NSF-funded multi-institutional project developing metabolomics as a functional genomics tool for elucidating the functions of Arabidopsis genes.

AcetoBase is a dedicated repository and curated database for the analysis of acetogenic bacteria based on the key functional gene formyltetrahydrofolate synthetase (FTHFS/fhs) of Wood-Ljungdahl Pathway for Acetogenesis.

Consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. The database is a useful platform for researchers studying the underlying mechanism for association among genetic ...

BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (support ...

An online database towards comprehensive essential gene annotation for prokaryotes.

Knowledge database of Soybean Functional gene Networks and miRNA functional networks.

Optimal allocation of HIV resources among geographical regions.

Database for human scaffold proteins.

A database of gene expression patterns in the Drosophila terminalia. An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster.

A toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. GOMCL is a tool to cluster and extract summarized associations of Gene Ontology based functions in omics data. It clusters GO terms using MCL ba ...

A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PRESDB:pig RNA Editing database

CancerLivER (Liver Cancer Expression Resource) is a database of liver cancer that maintains gene expression datasets and biomarkers curated from public repositories and literature respectively. It contains the following three modules for extracting a ...

Hierarchy and modularity in evolving metabolic networks. Enzyme recruitment is a fundamental evolutionary driver of modern metabolism. We see evidence of recruitment at work in the metabolic Molecular Ancestry Networks (MANET) database, an online re ...

an integrated resource for glycosyltransferase sequences and annotations. Glycosyltransferases (GTs), a large class of carbohydrate-active enzymes, adds glycosyl moieties to various substrates to generate multiple bioactive compounds, including natu ...

OGT Protein Interaction Network (OGT-PIN) is a curated and comprehensive database of experimentally identified interaction proteins of OGT and its orthologues in multiple species studied in the past several decades.

A database for the study of genomic reassortments among influenza viruses.

Human 51 672 molecular pathways database with tools for activity calculating and visualization.

A database dedicated to long-range genome interactions quality assessment.

YEASTRACT+ combines the existing database information of all yeast species, providing bioinformatics tools for the prediction and visualization of gene and genomic regulation based on orthologous regulatory associations described for other yeast spec ...

dBMHCC is a comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers.

DynLib is spectral database containing spectras from LC-MS runs for maize organs in order to investigate the metabolome.

A curated knowledgebase on the proteins that are involved in the blood coagulation pathway. It contains information on sequence, accession number, source, taxonomy, keywords, function, subcellular location, tissue specificity, associated diseases, mu ...

A database for construction and analysis of functional interaction networks for any species with a sequenced genome. Earth BioGenome Project has been officially launched in November 2018 with the goal of decoding genomes of Earth’s biome over a peri ...

Autophagy and Tumor Database (ATdb) is a database used to compile the published information concerning autophagy and tumor research. Such a database can be used for optaining an in-depth understanding of the complex correlations between autophagy and ...

a database of the Regulation of the Hippo Pathway in Cancer Genome. Hippo signaling pathway is a highly conserved pathway, which is consisted of a group of kinases. Dysregulation of Hippo signaling pathway is involved in the initiation and progressi ...

A Liver Disease Microarray Database, Visualization Platform and Data-Mining Resource. Providing Bioinformatics Data For The Study Of Liver Diseases. a liver disease microarray database, visualization platform and data-mining resource. Hepamine was ...

A Comprehensive Resource for Genetic Targets in Immune-Mediated Disease

A comprehensive database of trained immunity.

Model organism database for the bacterium Myxococcus xanthus.

A Comprehensive Resource for Targeted Proteomics Assays in the Community.

syngeneic mouse tumor database to model tumor immunity and immunotherapy response.

A database of human tissue functional gene networks built with a large compendium of curated RNA-seq data.

A host-pathogen interactome database for deciphering crucial molecular networks of wheat-common bunt cross-talk mechanisms.

A knowledgebase of human long non-coding RNAs with enhanced curation model and database system.

A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain.

Functional annotation of the first artificial organism Mycoplasma mycoides JCVI-syn3A.

The first integrated database of gene annotation and expression profiles for variants related to human diseases. An integrated database of variants and gene expression profiles for genetic diseases.

Cancer Gene and Pathway Explorer (CGPE) provides a highly integrated bioinformatics webserver for investigating, analyzing, and visualizing the TCGA and GEO gene expression data. CGPE provides key interactive and customizable analysis portal

BioModels Parameters is a resource that facilitates easy search and retrieval of parameter values used in the SBML models stored in the BioModels repository.

A manually curated database of polycystic ovarian syndrome. Nor Afiqah-Aleng, Sarahani Harun, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti-Azura Mohamed-Hussein, PCOSBase: a manually curated database of polycystic ovarian syndrome, Datab ...

Enabling systems immunology with a manually curated intercellular immune interaction network. ImmunoGlobe is a map of the immune network that describes how different parts of the immune system work together to drive immune responses. By structuring ...

An Alzheimer's Disease Biomarker Comprehensive Database for Humans. It includes the information for all the genetic parameters like mitochondrial genes, polymorphic genes (SNP's), transcription factors, proteins, miRNAs, Associative pathway, and AD b ...

ADEx: Autoimmune Diseases Explorer is a comprehensive and centralized database for exploring omics data in Autoimmune Diseases. The database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most ...

An Expertized Knowledge Database for the Model Legume Medicago truncatula. Medicago truncatula was proposed, about three decades ago, as a model legume to study the Rhizobium-legume symbiosis. It has now been adopted to study a wide range of biologi ...

NCI-Nature Pathway Interaction Database

DatumKB is a freely accessible database of experimental results involving the function and regulation of human proteins in cultured cells. The results are manually curated from biological research literature using a shorthand language and stored as d ...

Alzheimer’s disease (AD) pathophysiology is still imperfectly understood and current paradigms have not led to curative outcome. Omics technologies offer great promises for improving our understanding and generating new hypotheses. However, integrati ...

Huanglongbing (HLB) is a tritrophic disease complex involving citrus host trees, the Asian citrus psyllid (ACP) insect and a phloem restricted, bacterial pathogen Candidatus Liberibacter asiaticus (CLas). HLB is considered to be the most devastating ...

Docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases.

Comprehensive, user-friendly, and interactive web resource for analyzing cancer OMICS data.

A comprehensive resource for kiwifruit genomics.

A biocultural database combining biological pathways and historical linguistic data of Chinese Materia Medica for drug development.

Comprehensive and non-redundant benchmark for RNA–RNA docking and scoring.

A database of monosaccharide biosynthesis pathways. Monosaccharide Biosynthesis Pathways Database. Pathways for monosaccharide biosynthesis. Welcome to MonoPathDB, a database of biosynthesis pathways and enzymes for monosaccharides.

Mapping genes for calcium signaling and their associated human genetic disorders.

Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach.

A Database of Essential Genes Predicted Using Features From Interaction Networks.

A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes.

A platform dedicated to the visualization and analysis of protist co-expression and co-function networks.

The heterogeneous pharmacological medical biochemical network PharMeBINet.

A web platform to perform, learn, and discuss gene set analysis

ConnecTF is a platform to build gene networks by integrating transcription factor-target gene interactions.

Virtual Metabolic Human (VMH) database captures information on human and gut microbial metabolism and links this information to hundreds of diseases and nutritional data.

Database of human autophagy modulators with specific pathway and disease information.

CancerCRCdb is a comprehensive database of human core regulatory circuitry.

A high-throughput database of macromolecular host-pathogen interactions on the Web.

An integrated database for sex differences in cancer.

A database for comparative co-expression networks analysis of allohexaploid wheat and its progenitors.

A Database for Comparing Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors.

Multimorbidity is database of genetically interpretable comorbidities among common diseases in UK Biobank.

A Database Extension to Visualize Structural Interactome in One-to-many Manner

EMBF is a database of enzymes of microalgal biofuel feedstock.

An interactive resource of non-covalent contacts from over 100,000 publicly available crystal structures in the Protein Data Bank

Pathway analysis database of drug response based on phosphorylation activity measurements.

A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria.

ETph is a database for enhancer and their targets in pig and human.

A Database of Host-Pathogen Protein-Protein Interactions and Annotation Features of the Bacteria Causing Huanglongbing HLB Disease.

A comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis.

A curated database for comprehensively profiling methane cycling processes of environmental microbiomes.

DINAX is a comprehensive database of inherited ataxias.

ChemHub is a comprehensive database for selecting biosynthetic target molecules based on compound functions.

A Manually Curated Database of Human Ophthalmic Diseases with Symptom Characteristics and Genetic Variants Towards Facilitating Quick and Definite Diagnosis.

A comprehensive and interactive database for transcriptomes from prostate cancer population cohorts.

A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1.

MitopatHs is a database that allows to navigate among the biochemical pathways (PatHs) of human (H) mitochondria (Mito). It is a logically-framed tool for visualizing multiple mitochondrial pathways.

An integrated resource for dedicating to genetic variants, gene expression and epigenetic factors of human eye diseases.

Plant transfer RNA-derived non-coding RNAs (tncRNAs) database.

A universal platform for annotating and analyzing non-classically secreted proteins of Gram-positive bacteria

Database for identifying, genotyping, and modelling the associations between single nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans.

A comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation.

An expression knowledgebase at single cell/nucleus level for the discovery of coding-noncoding RNA functional interactions in skeletal muscle.

A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons. A Database of miRNAs during Muscular Atrophy. Defence Institute of Physiology and Allied Sciences,.

Quickomics is a tool for exploring omics data in an intuitive, interactive and informative manner.

One-stop and comprehensive annotation system for individual cancer genome at multi-omics level.

A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication.

emiRIT is a text-mining based database for microRNA information.

Stress Knowledge Map: A compilation of knowledge on mechanisms underlying responses of plants to stress, the so called stress signalling network.

ERMer: A serverless platform for navigating, analyzing, and visualizing Escherichiacoli regulatory landscape through graph database.

A resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs.

MetAMDB is a software/database for the analysis of metabolic models and specifically the work with atom mappings.

Branch of BioModels Database dedicated to hosting models automatically generated from pathway resources, such as KEGG, BioCarta, MetaCyc, PID and SABIO-RK.

ModelMatcher is a scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research.

A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.

DrugSimDB is a comprehensive database of multi-modal drug similarity measures by integrating variety of heterogenous datasets.

CovPDB, a database solely dedicated to high-resolution cocrystal structures of biologically relevant cP–L complexes, curated from the Protein Data Bank

BCGene is a online database for brain cancer-implicated genes: exploring the subtype-specific mechanisms of brain cancer

a comprehensive genetic database of Parkinson's disease. Gene4PD: an integrative genomic database and analytic platform for Parkinson's disease. Rare variants identified from PD patients.

Curated proteolytic events and pathways from the literature.

ATLASx is a computational map for the exploration of biochemical space ATLASx databases explore potential biochemical reactions within different chemical scopes: bioDB, bioATLAS, and chemATLAS.

A database of gene-disease pathway association, along with tools to identify i) disease-disease comorbidity, ii) pathway enrichment, iii) disease enrichment, iv) disease enrichment using GO terms, v) polypharmacological target prediction and vi) Venn ...

PharmOmics is a A Species- and Tissue-specific Drug Signature Database and Online Tool for Toxicity Prediction and Drug Repurposing. It is a Web server for Identifying Pathological Pathways, Networks, and Key Regulators via Multidimensional Data Inte ...

A Genome-wide Positioning Systems Platform to Catalyze Multi-omics for Alzheimer’s Therapeutic Discovery. A Network-based multi-omics analysis informs Alzheimer's patient care and therapeutic development.

A renovated knowledgebase for deriving biological and chemical insight from genes, proteins, and metabolites.

The database revolves around the protein structure of catalytic PDE domains and the way PDE inhibitors can interact with them. It contains a systematic analysis of all phosphodiesterase (PDE) catalytic domain crystal structures present in the Protein ...

Dr AFC is a tool for drug repositioning through anti-fibrosis characteristic.

Phylogenize is a web tool that allows users to link microbial genes to environments, accounting for phylogeny. More specifically, given community composition data, phylogenize links genes in microbial genomes to either microbial prevalence in, or sp ...

The CerealESTdb, a user-friendly, searchable, and interactive database has been developed with a primary goal to provide information on assembled and annotated ESTs from four major crop plants, namely wheat, rice, maize, and sorghum under multiple en ...

High performance search engine for gene expression. It integrates thousands of manually curated, well described public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts such as diseases, drug ...

EchinoDB is a database consisting of amino acid sequence othoclusters from 42 echinoderm transcriptomes. We sampled taxa to span the deepest divergences within each of the 5 extant echinoderm classes. Data can be searched by keywords such as annotati ...

TFcancer is a manually curated database of transcription factors associated with human cancer. TFcancer features in comprehensive annotations of TFs in human cancers. TFcancer mainly focused on the influence of transcription factors on four dimension ...

A Server Platform For High Altitude Human miRNA-Gene Coregulatory Networks And Associated Regulatory-Circuits. HAHmiR DB (High-Altitude Human miRNA Database) is a unique, comprehensive, curated collection of miRNAs that have been experimentally vali ...

Accurate Prediction of Kinase-Substrate Networks Using Knowledge Graphs. Abstract Phosphorylation of specific substrates by protein kinases is a key control mechanism for vital cell-fate decisions and other cellular processes. However, discovering s ...

AREAdata is a worldwide climate dataset averaged across spatial units at different scales through time. It is a PearseLab data resource where you can download daily estimates of climate/environmental data which have been averaged across different lev ...

Automated annotation of amino acid biosynthesis | Abstract GapMind is a web-based tool for annotating amino acid biosynthesis in bacteria and archaea ( http: papers.genomics.lbl gov gaps ). GapMind incorporates many variant pathways and 130 different ...

TCM-Blast for traditional Chinese medicine genome alignment with integrated resources.

YPIBP is an inclusive database consisting of all the members of phosphatidylinositols-binding proteins which are collected from high-throughput proteome and lipid array studies, QuickGO and a rigorous literature mining. Cumulatively, across all PI, t ...

Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons.

DataBase of Plant Research (DBHR) is an online data resource specifically designed for human research, which provides access to almost all latest human database on easy and friendly finding way, the classification based on data type is informative an ...

A high-quality SNV database for interspecies genetic divergence investigation among macaques. A database for genetic divergence investigation among macaques. MACSNVdb is an open-access SNV database comprising ~74.51 million high-quality non-redunda ...

Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB. PrecocityDB Database and enrichment analysis of genes associated with precocious puberty The SQL file of database is stored as ZIP file precocity.zip ...

A Functional Analysis Tools for Post-translational Modifications (FAT-PTM) database, which supports data from publicly available proteomic analyses encompassing eight different types of PTMs and over 49,000 PTM sites.

VaximmutorDB is database for vaccine immune factors. A "vaximmutor" is coined here to represent an immune factors that is triggered by a vaccination and plays a role in vaccine-induced host immunity. Vaximmuntors are specifically targeted by the inna ...

Sift-PUL database is a public repository providing predicted PULs with specific functional annotations. The key difference between sift-PUL and other PUL databases (e.g. PULDB, CGCs and dbCAN-PUL) is the functional annotation for each predicted PUL.

Co-expression Network Database for <i>de novo</i> Transcriptome Assembly of <i>Paeonia lactiflora</i> Pall. Paeonia lactiflora Pall., commonly known as the herbaceous peony, is an ornamental flowering plant known around the world. Its oil contains a ...