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https://adastra.autosome.ru/zanthar
Landscape of allele specific transcription factor binding in human genome. Creators conducted meta analysis of ChIP-Seq experiments and assembled database of allele specific binding events listing more than half million entries at nearly 270 thousand single nucleotide polymorphisms for several hundred human transcription factors and cell types.
Proper citation: Allelic Dosage corrected Allele Specific human Transcription factor binding sites (RRID:SCR_021863) Copy
https://jcr.clarivate.com/JCRLandingPageAction.action
Web tool with systematic, objective means to critically evaluate journals, with quantifiable, statistical information based on citation data. Provides information about academic journals in natural sciences and social sciences, including impact factors in database integrated with Web of Science. Sourced from Web of Science Core Collection,citation index on Web of Science platform.
Proper citation: Journal Citation Reports (RRID:SCR_017656) Copy
http://biocc.hrbmu.edu.cn/CellMarker/
Database provides cell markers for various cell types in tissues of human and mouse. Manually curated resource of cell markers in human and mouse. Provides user-friendly interface for browsing, searching and downloading markers of diverse cell types of different tissues. Summarized marker prevalence in each cell type is graphically presented., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CellMarker (RRID:SCR_018503) Copy
General purpose, document based, distributed database built for modern application developers and for the cloud. Offers Community and Enterprise version of database.MongoDB Community is source available and free to use edition of MongoDB. MongoDB Enterprise is available as part of MongoDB Enterprise Advanced subscription and includes comprehensive support for your MongoDB deployment. MongoDB Enterprise also adds enterprise-focused features such as LDAP and Kerberos support, on-disk encryption, and auditing.MongoDB also offers Atlas,hosted MongoDB Enterprise service option in cloud which requires no installation overhead and offers free tier to get started.
Proper citation: MongoDB (RRID:SCR_021224) Copy
https://www.grnpedia.org/trrust/
TRUSST is reference database of human transcriptional regulatory interactions.TRRUST v2 is manually curated expanded reference database of human and mouse transcriptional regulatory interactions.
Proper citation: Transcriptional Regulatory Relationships Unrevealed by Sentence based Text mining database (RRID:SCR_022554) Copy
http://www.mirtoolsgallery.org/miRToolsGallery/node/1055
Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: miRanda (RRID:SCR_017496) Copy
https://www.grnpedia.org/trrust/Network_search_form.php
Reference database of human transcriptional regulatory interactions. Manually curated database of human and mouse transcriptional regulatory networks.
Proper citation: TTRUST (RRID:SCR_022490) Copy
Comprehensive resource of neuropeptides, which holds non-redundant neuropeptide entries. Data collected from resources including MEDLINE abstracts, full papers, UniProt,database at www.neuropeptides.nl and Neuropedia. Contains detailed annotations for each entry, including source organisms, tissue specificity, families, names, post-translational modifications, 3D structures and literature references. Amino acid compositions, isoelectric points, molecular weight and other physicochemical properties of peptides are also provided. Search database with keywords such as sequence, name, family, etc.,User friendly web tools like browsing, sequence alignment and mapping are also integrated.Users can submit new entries online. Each new entry is validated before incorporating it.
Proper citation: NeuroPep (RRID:SCR_023102) Copy
Public knowledge base for information on evolutionary timescale of life. Data from thousands of published studies are assembled into searchable tree of life scaled to time.
Proper citation: TimeTree (RRID:SCR_021162) Copy
http://opig.stats.ox.ac.uk/webapps/newsabdab/sabdab/
Database containing all antibody structures available in the PDB, annotated and presented in consistent fashion.Each structure is annotated with number of properties including experimental details, antibody nomenclature (e.g. heavy-light pairings), curated affinity data and sequence annotations. You can use the database to inspect individual structures, create and download datasets for analysis, search the database for structures with similar sequences to your query, monitor the known structural repetoire of antibodies.
Proper citation: Structural Antibody Database (RRID:SCR_022096) Copy
http://viewer.shigen.info/cgi-bin/crispr/crispr.cgi
Web tool to show micro homology sequences striding over double strand break point created by CRISPR/Cas9 system. Used to search for CRISPR target site with micro-homology sequences. Used to predict deletion pattern.
Proper citation: NBRP Medaka CRISPR target site (RRID:SCR_018159) Copy
http://bioinfo.life.hust.edu.cn/EVmiRNA/#!/
Collection of comprehensive miRNA expression profiles in extracellular vesicles from tissues. Includes miRNA expression profiles, miRNA regulated pathways, miRNA function, miRNA related drugs and publications to support miRNA biomarker discovery.
Proper citation: EVmiRNA (RRID:SCR_018795) Copy
Database lists names of prokaryotes that have been validly published in International Journal of Systematic and Evolutionary Microbiology directly or by inclusion in Validation List, under Rules of International Code of Nomenclature of Bacteria. Has classification of prokaryotes and information on prokaryotic nomenclature and culture collections.
Proper citation: LPSN Database (RRID:SCR_018151) Copy
Database by Medisapiens Ltd. as fully integrated and annotated human gene expression data source. All genes are comparable across all samples. Provides data analysis options using database of human transcriptome.
Proper citation: IST Online (RRID:SCR_018794) Copy
https://prokoplab.com/vistedd/
Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein.
Proper citation: Viral Integrated Structural Evolution Dynamic Database (RRID:SCR_018793) Copy
Gene atlas of Type 2 Diabetes Mellitus associated complex disorders. Provides curated and integrated information about genes involved in development and progression of Type 2 Diabetes Mellitus, genes and pathways with evidence for role in diabetes under risk factors including obesity, diet, inflammation, stress and complex disorders that are associated with Type 2 Diabetes Mellitus including atherosclerosis, diabetic retinopathy, diabetic nephropathy, diabetic neuropathy, cardiovascular disease.
Proper citation: T2DiACoD (RRID:SCR_019092) Copy
https://www.mcdb.ucla.edu/Research/Hartenstein/dbla/index.html
Atlas providing structure and development of Drosophila brain lineages. Used to learn about projection pattern of lineages as first step towards reconstructing and understanding all neurons.
Proper citation: Drosphila Brain Lineage Atlas (RRID:SCR_017507) Copy
https://github.com/clinwiki-org/clinwiki
Clinical trials database.
Proper citation: ClinWiki (RRID:SCR_021297) Copy
https://www.osha.gov/chemicaldata/
Chemical inventory for occupational chemical information. Collects information from several government agencies and organizations. Includes information about identification and physical properties, exposure limits, sampling.
Proper citation: OSHA Occupational Chemical Database (RRID:SCR_018203) Copy
https://www.epicore.ualberta.ca/IsletCore/
Collection of data from all pancreatic islet isolations.
Proper citation: Alberta Diabetes Institute IsletCore database (RRID:SCR_018566) Copy
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