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http://www.mir2disease.org/

A manually curated database, aims at providing a comprehensive resource of miRNA deregulation in various human diseases. Each entry in the miR2Disease contains detailed information on a miRNA-disease relationship, including miRNA ID, disease name, a brief description of the miRNA-disease relationship, miRNA expression pattern in the disease state, detection method for miRNA expression, experimentally verified miRNA target gene(s), and literature reference . All entries can be retrieved by miRNA ID, disease name or target gene. miR2Disease will be updated bimonthly. miR2Disease sincerely looks forward to recently established relationship between miRNA and human diseases to be submitted.

Proper citation: miR2Disease (RRID:SCR_007792) Copy   

•   Source: SciCrunch Registry

http://mirgator.kobic.re.kr/

Database of compiled, public, deep sequencing miRNA data and several novel tools to facilitate exploration of massive data. The miR-seq browser supports users to examine short read alignment with the secondary structure and read count information available in concurrent windows. Features such as sequence editing, sorting, ordering, import and export of user data are of great utility for studying iso-miRs, miRNA editing and modifications. miRNA����??target relation is essential for understanding miRNA function. Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample, is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets.

Proper citation: miRGator (RRID:SCR_007793) Copy   

•   Source: SciCrunch Registry

http://www.noncode.org/

Collection of non-coding RNAs (excluding tRNAs and rRNAs) as an integrated knowledge database. Used to get text information such as class,name,location,related publication,mechanism through which it exerts its function, view figures which show their location in the genome or in a specific DNA fragment, and the regulation elements flanking the ncRNA gene sequences.

Proper citation: NONCODE (RRID:SCR_007822) Copy   

•   Source: SciCrunch Registry

http://networkin.info/

A method for predicting in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins. This website allows a user to browse/search and investigate predictions made using the NetworKIN algorithm. The site is powered by the latest phosphoproteome in Phospho.ELM. Alternatively users can submit their own protein sequences and phosphorylation sites and obtain new NetworKIN predictions.

Proper citation: NetworKIN (RRID:SCR_007818) Copy   

•   Source: SciCrunch Registry

http://www.p3db.org

It was established with an overall objective to provide a resource of protein phosphorylation data from multiple plants. P3DB was constructed with a dataset from oilseed rape. The data was obtained using a combination of data-dependent neutral loss and multistage activation mass spectrometry. The dataset includes 14,670 non-redundant phosphorylation sites from 8,894 phospho-peptides in 6,382 substrate proteins.

Proper citation: Plant Protein Phosphorylation Database (RRID:SCR_007841) Copy   

•   Source: SciCrunch Registry

http://www.comparative-legumes.org/

LIS is a publicly accessible legume resource that integrates genetic and molecular data from multiple legume species and enables cross-species genomic, transcript and map comparisons. The intent of the LIS is to help researchers leverage data-rich model plants to fill knowledge gaps across crop plant species and provide the ability to traverse between interrelated data types. LIS, a component of the Model Plant Initiative (MPI), is being developed as part of a cooperative research agreement between the National Center for Genome Resources (NCGR) and the USDA Agricultural Research Service (ARS).

Proper citation: Legume Information System (RRID:SCR_007761) Copy   

•   Source: SciCrunch Registry

http://greengenes.secondgenome.com/downloads

Database that provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. The 16S rRNA gene database provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. ARB users can use Greengenes to update local databases., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Greengenes (RRID:SCR_002830) Copy   

•   Source: SciCrunch Registry

http://www.wormatlas.org/

Anatomical atlas about structural anatomy of Caenorhabditis elegans. Provides simple interface allowing user to easily navigate through every anatomical structure of worm. Contains set of images which can be sorted by different characteristics: sex, genotype, age, body portion or tissue type. Includes links to other major worm websites and databases. Application for viewing and downloading thousands of unpublished electron micrographs and associated data. These images have been generated by several labs in the C. elegans community, including the MRC, the Hall lab (Center for C. elegans Anatomy), and the Culotti and Riddle labs.

Proper citation: WormAtlas (RRID:SCR_002861) Copy   

•   Source: SciCrunch Registry

http://viperdb.scripps.edu/

Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: VIPERdb (RRID:SCR_002853) Copy   

•   Source: SciCrunch Registry

http://eggnog.embl.de

A database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). eggNOG's database currently counts 1.7 million orthologous groups in 3686 species, covering over 7.7 million proteins (built from 9.6 million proteins). (Jan 30, 2014)

Proper citation: eggNOG (RRID:SCR_002456) Copy   

•   Source: SciCrunch Registry

http://ndbserver.rutgers.edu/

A database of three-dimensional structural information about nucleic acids and their complexes. In addition to primary data, it contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. NDB maintains the macromolecular Crystallographic Information File (mmCIF).

Proper citation: Nucleic Acid Database (RRID:SCR_003255) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/

Compendium of protein fingerprints. Diagnostic fingerprint database.

Proper citation: PRINTS (RRID:SCR_003412) Copy   

•   Source: SciCrunch Registry

http://www.genpat.uu.se/mtDB

A database of human mitochondrial genomes containing mtDNA sequences, polymorphic sites, and the ability to search for specific variants. It contains 1865 complete sequences and 839 coding region sequences.

Proper citation: mtDB - Human Mitochondrial Genome Database (RRID:SCR_002945) Copy   

•   Source: SciCrunch Registry

http://mirnamap.mbc.nctu.edu.tw

A database of experimentally verified microRNAs and miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3'-UTR of genes. In order to reduce the false positive prediction of miRNA targets, several criteria are supported for filtering the putative miRNA targets. Furthermore, miRNA expression profiles can provide valuable clues for investigating the properties of miRNAs, such tissue specificity and differential expression in cancer/normal cell. Therefore, we performed the Q-PCR experiments for monitoring the expression profiles of 224 human miRNAs in eighteen major normal tissues in human. The cross-reference between the miRNA expression profiles and the expression profiles of its target genes can provide effective viewpoint to understand the regulatory functions of the miRNA.

Proper citation: miRNAMap (RRID:SCR_003156) Copy   

•   Source: SciCrunch Registry

http://compbio.uthsc.edu/miRSNP/

Database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization. SNPs and INDELs in miRNAs and their target sites may affect miRNA-mRNA interaction, and hence affect miRNA-mediated gene repression. The PolymiRTS database was created by scanning 3'UTRs of mRNAs in human and mouse for SNPs and INDELs in miRNA target sites. Then, the potential downstream effects of these polymorphisms on gene expression and higher-order phenotypes are identified. Specifically, genes containing PolymiRTSs, cis-acting expression QTLs, and physiological QTLs in mouse and the results of genome-wide association studies (GWAS) of human traits and diseases are linked in the database. The PolymiRTS database also includes polymorphisms in target sites that have been supported by a variety of experimental methods and polymorphisms in miRNA seed regions.

Proper citation: PolymiRTS (RRID:SCR_003389) Copy   

•   Source: SciCrunch Registry

http://www.microbial-ecology.net/probebase/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A database of probes and microbes that can be searched for target organisms, probe names, probe sequences, probe accession numbers, and references. The search target site function can assist in the development of new rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization (FISH), while the match tool can be used to rapidly retrieve all published probes targeting your query sequences (e.g. from a rRNA gene clone library) without prior phylogenetic analysis. probeBase is hyperlinked with PubMed, RDP-II, and Greengenes to provide additional bibliographic information and up-to-date data on probe specificity. Ribosomal RNA (rRNA) targeted oligonucleotide probes are widely used for fluorescence in situ, dot blot, and microarray hybridization in culture-independent studies of microbial communities and for the identification of uncultured prokaryotes in clincal and environmental samples. probeBase is a comprehensive database containing published rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information.

Proper citation: probeBase (RRID:SCR_003417) Copy   

•   Source: SciCrunch Registry

http://www.phi-base.org/

Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC).

Proper citation: PHI-base (RRID:SCR_003331) Copy   

•   Source: SciCrunch Registry

http://www.mitomap.org/

Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf.

Proper citation: MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) Copy   

•   Source: SciCrunch Registry

http://www.netpath.org/

A manually curated resource of signal transduction pathways in humans. All pathways are freely available for download in BioPAX level 3.0, PSI-MI version 2.5 and SBML version 2.1 formats. The slim pathway models representing only core reactions in each pathway are available at NetSlim. All the NetPath pathway models are also submitted to WikiPathways., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NetPath (RRID:SCR_003567) Copy   

•   Source: SciCrunch Registry

http://sideeffects.embl.de/

Database containing information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug-target relations. The SIDER Side Effect Resource represents an effort to aggregate dispersed public information on side effects. To our knowledge, no such resource exist in machine-readable form despite the importance of research on drugs and their effects. The creation of this resource was motivated by the many requests for data that we received related to our paper (Campillos, Kuhn et al., Science, 2008, 321(5886):263-6.) on the utilization of side effects for drug target prediction. Inclusion of side effects as readouts for drug treatment should have many applications and we hope to be able to enhance the respective research with this resource. You may browse the drugs by name, browse the side effects by name, download the current version of SIDER, or use the search interface.

Proper citation: SIDER (RRID:SCR_004321) Copy   

•   Source: SciCrunch Registry