Tag: molecular interactions, pathways and networks


Found 220 sources
Source Match ReputationScore*

Kyoto Encyclopedia of Genes and Genomes


KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by geno ...
100%

Reactome - a curated knowledgebase of biological pathways


REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database.
95%

Biological General Repository for Interaction Datasets


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.
93%

IUPHAR/BPS Guide to PHARMACOLOGY


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 ...
92%

Comparative Toxicogenomics Database


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 ...
85%

Molecular INTeraction database


MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. As of September 2013, This resource uses the IntAct database framework to help reduce the effort of scientists and improve o ...
83%

Disease Ontology


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 ...
80%

Database of Interacting Proteins


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
80%

WikiPathways


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.
78%

DisGeNET: a knowledge base for disease genomics


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 ...
77%

DAVID Bioinformatics Resources


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.
75%

Saccharomyces Genome Database


The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. SGD contains a variety of biological information and tools with which to search and analyze it.
74%

Human Protein Reference Database


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 ...
70%

TRANSFAC


Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.
69%

NCBI Gene


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 ...
69%

BioModels


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 ...
69%

Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants


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 ...
66%

MetaCyc


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 ...
65%

Pathway Commons


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 ...
65%

GeneCards: human genes, protein and diseases


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.
65%

Rat Genome Database


The Rat Genome Database is the premier site for genetic, genomic, phenotype, and disease data generated from rat research. It provides easy access to corresponding human and mouse data for cross-species comparison and its comprehensive data and innov ...
64%

Xenopus laevis and tropicalis biology and genomics resource


Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. It includes gene expression patterns that incorporate image data from the li ...
63%

TarBase


DIANA-TarBase was initially released in 2006 and it was the first database aiming to catalogue published experimentally validated miRNA:gene interactions. DIANA-TarBase (v7.0), provides hundreds of thousands of high quality manually curated experimen ...
62%

Search Tool for Interactions of Chemicals


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.
62%

BiGG Models


BiGG is a freely compendium of published genome-scale metabolic networks, combined into a single database. NCBI genome annotations are used to map genes, and metabolites are linked to many external databases such as KEGG, PubChem as well as others..
60%

Rhea


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 ...
60%

Small Molecule Pathway Database


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, ...
59%

EcoCyc E. coli Database


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 ...
57%

Interologous Interaction Database


I2D (Interologous Interaction Database) is a database of known and predicted mammalian and eukaryotic protein-protein interactions (PPIs).
57%

NCBI


The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information
57%

SuperTarget


Drug-related information: medical indications, adverse drug effects, drug metabolism and Gene Ontology terms of the target proteins.
57%

miRTarBase


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 ...
55%

VirHostNet 2.0


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.
55%

Yeast Searching for Transcriptional Regulators and Consensus Tracking


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 ...
55%

Mammalian Gene Collection


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 ...
55%

MatrixDB: Extracellular Matrix Interaction Database


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 ...
55%

Database of Bacterial Exotoxins for Human


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.
55%

SIGnaling Network Open Resource


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 ...
55%

BioSystems


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 ...
54%

Interferome


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 ...
54%

RegulonDB


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 ...
54%

H-Invitational Database


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 ...
54%

Sol Genomics Network


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.
53%

Phospho.ELM


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.
53%

Candida Genome Database


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 ...
53%

MiST 3.0: Microbial Signal Transduction database


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 ...
52%

SABIO-RK Biochemical Reaction Kinetics Database


SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.
52%

Protein Interaction Network Analysis platform


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 ...
52%

3D interacting domains


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 ...
52%

Integrated Pathway Analysis and Visualization System


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 ...
52%

MetaNetX


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 ...
51%

BIND: The Biomolecular Interaction Network Db


Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.
51%

zfishbook


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.
51%

StarBASE


microRNA-mRNA interaction maps
51%

BioCyc


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 ...
51%

Legume Information System


The Legume Information System (LIS) is a collaborative, community resource to facilitate crop improvement by integrating genetic, genomic, and trait data across legume species.
51%

GeneWeaver


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 ...
50%

GenomeNet


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).
50%

GWASdb


GWASdb comprises of collections of traits/diseases associated SNP (TASs) from current GWAS and their comprehensive functional annotations, as well as disease classifications.
50%

Toxin and Toxin Target Database


Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.
49%

MicrobesOnline


A suite of Web-based tools for comparative genomics
49%

The Arabidopsis Gene Regulatory Information Server


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 ...
48%

FlyCircuit


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 ...
48%

Network of Cancer Genes


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 ...
48%

PlnTFDB


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 ...
48%

DNASU Plasmid Repository


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 ...
47%

CoryneRegNet 6.0 - Corynebacterial Regulation Network


Corynebacterial Regulation Network a reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks.
47%

Signaling Pathway Integrated Knowledge Engine


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 ...
47%

Autism Knowledgebase


Autism genetics KnowledgeBase, an evidence-based knowledgebase of autism genetics.
46%

Pocketome: an encyclopedia of small-molecule binding sites in 4D


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 ...
46%

Interolog Regulog Database


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.
46%

Comprehensive Yeast Genome Database


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 ...
46%

Protein-Chemical Structural Interactions


Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight.
46%

RegPrecise


Predicted regulons in prokaryotic genomes
46%

Tomato Functional Genomics Database


The Tomato Functional Genomics Database integrates several prior databases including the Tomato Expression Database and Tomato Metabolite Database, and the Tomato Small RNA Database.
46%

UniProtKB Swiss-Prot


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.
45%

Nematode.net


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 ...
45%

BacMap


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.
45%

Affymetrix NetAffx Analysis Center


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.
45%

DroID - Drosophila Interactions Database


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, ...
45%

NucleaRDB


Families of nuclear hormone receptors
44%

Bacterial Protein Interaction Database


Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.
44%

SuperCYP


Cytochrome P450 alleles and drug interactions
44%

PathBank


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 ...
44%

MetaCrop 2.0


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. ...
44%

Saccharomyces cerevisiae Transcription Factor Database


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 ...
44%

DOMINE


Known and predicted protein domain interactions observed in PDB entries,
43%

PROMISCUOUS


Protein-protein and drug-protein interactions for studies of drug repositioning
43%

CCDB


Cervical cancer gene database
43%

SwissLipids


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.
42%

IBIS


Inferred Biomolecular Interaction Server: protein-protein, ligand- and nucleic acid-binding sites
42%

PreOpDB


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 ...
42%

BioMart Central


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 ...
42%

DRYGin


Data Repository for Yeast Genetic Interaction Networks
42%

COXPRESdb


Coexpressed genes and networks in human and mouse
42%

University of Minnesota Biocatalysis/Biodegradation Database


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 ...
42%

Multi Experiment Matrix (MEM)


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 ...
42%

Negatome


A database of non-interacting proteins
42%

ProtCID


Protein Common Interface Database
42%

PepX


A non-redundant database of protein-peptide complexes
42%

HitPredict


Quality assessed protein-protein interactions in 9 species
41%

CADgene


Coronary Artery Disease gene database
41%

WebGeSTer DB


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 ...
41%

phiSITE


Gene regulation in bacteriophages
41%

CancerResource


Cancer-relevant proteins and compound interactions
41%

TcoF-DB


Database for Human Transcription Co-Factors
41%

CyanoBase


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 ...
41%

RegPhos


Regulatory Network in Protein Phosphorylation
41%

UCSC Cancer Genomics Browser


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 ...
41%

PAIR


Predicted Arabidopsis Interactome Resource
41%

Death Domain Database


Death Domain Database is a manually curated database of protein-protein interactions for Death Domain Superfamily.
41%

P2CS


Prokaryotic 2-Component Systems database
41%

DISNOR


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 ...
40%

REPAIRtoire


DNA repair pathways of human, yeast and E.coli
40%

dbCRID


Database of Chromosomal Rearrangements In Diseases
40%

Arabidopsis Hormone 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 ...
40%

KaPPA-View


Kazusa Plant Pathway Viewer
40%

PolygenicPathways


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 ...
40%

Isobase


IsoRank PPI Network Alignment Based Ortholog Database
40%

BINDTranslation


A database of curated biomolecular interactions.
40%

Human Integrated Pathway 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 ...
40%

DIMA


Domain interaction map: experimental and predicted protein domain interactions
39%

MMMDB


Mouse Multiple Tissue Metabolomics Database
39%

ADPriboDB


ADP-ribosylated proteins and sites
39%

AtPID


Arabidopsis thaliana Protein Interactome Database
39%

GWIDD


Genome-WIde Docking Database: 3D structures of protein complexes
39%

LSD


This database contains senescence associated genes (SAGs) from 21 species retrieved based on genetic, genomic, proteomic, physiological or other experimental evidence, and classified into different categories according to their functions in leaf sene ...
39%

Stem Cell Discovery Engine


Comparison system for cancer stem cell analysis
39%

FunSimMat


Gene Ontology-based functional similarity values for proteins and protein families
39%

RSSsite


Reference database and prediction tool for the identification of cryptic recombination signal sequences (RSSs) in the human and mouse genomes.
38%

miRPathDB


Dictionary on miRNAs and their putative target pathways
38%

Yeast KID


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.
38%

SpliceDisease DB


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 ...
38%

DDPC


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 ...
38%

DNAtraffic


A database for systems biology of DNA dynamics during the cell life.
38%

miRGator v2.0


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 ...
38%

DOMMINO


Database of MacroMolecular INteractions
38%

TRIP


Protein-protein interactions for mammalian TRP channels
38%

GeMInA


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 ...
38%

GeneTests


A medical genetics information resource developed for physicians, other healthcare providers, and researchers, available at no cost to all interested persons.
38%

PsyGeNET


Psychiatric disorders and Genes association NETwork. Exploratory analysis of psychiatric diseases and their associated genes.
38%

FragmentStore


Comprehensive database of fragments linking metabolites, toxic molecules and drugs
38%

CircFunBase


Database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions.
37%

KUPS


Interacting and non-interacting protein pairs
37%

TriForC database


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 ...
37%

Plant Reactome


Plant metabolic, regulatory and signaling pathways
37%

ePlant


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.
37%

KnockTF


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 ...
37%

AlgaePath


Comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae.
37%

NPInter v4.0


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 ...
37%

XTalkDB


Crosstalk among signaling pathways
36%

BISC


Binary SubComplexes in Proteins Database
36%

Agronomic Linked Data


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 ...
36%

rSNP_Guide


A system of databases documenting the influence of mutations in regulatory gene regions.
36%

Diseasecard


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 ...
36%

CoNekT-Plants


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
36%

RNAct


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 ...
36%

PlantCircNet


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 ...
35%

AtMAD


Arabidopsis thaliana Multi-omics Association Database
35%

PlantMetabolomics


An NSF-funded multi-institutional project developing metabolomics as a functional genomics tool for elucidating the functions of Arabidopsis genes.
35%

VnD


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 ...
35%

RetroRules


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 ...
35%

ConsensusPathDB


Database for integration of human functional interactions
35%

Datanator


Datanator is an integrated database of molecular data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for data-driven analyses and mechanistic models. Datanator includes ...
35%

SoyFN


Knowledge database of Soybean Functional gene Networks and miRNA functional networks.
35%

AppleMDO


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 ...
35%

ePath


An online database towards comprehensive essential gene annotation for prokaryotes.
34%

ScaPD


Database for human scaffold proteins.
34%

Fly Terminalia Database


A database of gene expression patterns in the Drosophila terminalia. An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster.
34%

ARGminer


ARGminer is a web platform dedicated to the validation of ARGs by using sequence alignment and evidence from multiple sources.
34%

HIV-related


Optimal allocation of HIV resources among geographical regions.
34%

LOGIQA


A database dedicated to long-range genome interactions quality assessment.
34%

SalMotifDB


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
34%

Clotbase


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 ...
34%

Xanthusbase


Model organism database for the bacterium Myxococcus xanthus.
33%

SCDevDB


A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PRESDB:pig RNA Editing database
33%

AcetoBase


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.
33%

MANET


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 ...
33%

BiomeNet


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 ...
33%

PCOSBase


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 ...
33%

Alzheimers Disease Biomarker Comprehensive Database (ABCD)


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 ...
33%

GTDB


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 ...
33%

LeGOO


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 ...
33%

RHPCG


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 ...
33%

PID


NCI-Nature Pathway Interaction Database
32%

GRNdb


TF-target relationsips inferred from single cell and bulk RNA-seq datasets
32%

BioSimulators


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 ...
32%

KLIFs


Kinase-ligand Interaction Fingerprints and Structures
32%

Citrusgreening.org


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 ...
32%

FluReassort


A database for the study of genomic reassortments among influenza viruses.
30%

ASNR


Animal Social Networks Repository - repository of interaction data from published studies of wild, captive, and domesticated animals.
30%

DDAP


Docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases.
30%

UALCAN


Comprehensive, user-friendly, and interactive web resource for analyzing cancer OMICS data.
30%

RRDB


Comprehensive and non-redundant benchmark for RNA–RNA docking and scoring.
30%

The Ca2+ genome database


Mapping genes for calcium signaling and their associated human genetic disorders.
30%

GlycoPathDB


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.
30%

HAMdb


Database of human autophagy modulators with specific pathway and disease information.
30%

SCMVTDb


Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach.
30%

VMH


Virtual Metabolic Human (VMH) database captures information on human and gut microbial metabolism and links this information to hundreds of diseases and nutritional data.
30%

Protein Contacts Atlas


An interactive resource of non-covalent contacts from over 100,000 publicly available crystal structures in the Protein Data Bank
30%

SpirPro


A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1.
30%

SeattleSNPs variation discovery resource


Database for identifying, genotyping, and modelling the associations between single nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans.
30%

Path2Models


Branch of BioModels Database dedicated to hosting models automatically generated from pathway resources, such as KEGG, BioCarta, MetaCyc, PID and SABIO-RK.
30%

ImmunoDB


A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.
30%

Gene4PD


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.
30%

PMAP-CutDB proteolytic event database


Curated proteolytic events and pathways from the literature.
30%

PharmOmics


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 ...
30%

AlzGPS


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.
30%

PDEStrIAn


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 ...
30%

phylogenize


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 ...
30%

ADEx: Autoimmune Diseases Explorer


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 common autoimmune diseases.
30%

ATdb


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 ...
30%

Genevestigator


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 ...
30%

HAHmiR DB


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 ...
30%

LinkPhinder


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 ...
30%

HisgAtlas


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 ...
30%

GapMind


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 ...
30%

GOMCL


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 ...
30%

Hepamine


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 ...
30%

HpeNet


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 ...
30%

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