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http://pepr.cnmcresearch.org/

An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ).

Proper citation: Public Expression Profiling Resource (RRID:SCR_007274) Copy   

•   Source: SciCrunch Registry

http://epiexplorer.mpi-inf.mpg.de/

A web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborious preprocessing.

Proper citation: EpiExplorer (RRID:SCR_007301) Copy   

•   Source: SciCrunch Registry

http://compbio.soe.ucsc.edu/yeast_introns.html

Database of information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Listed are known spliceosomal introns in the yeast genome and the splice sites actually used are documented. Through the use of microarrays designed to monitor splicing, they are beginning to identify and analyze splice site context in terms of the nature and activities of the trans-acting factors that mediate splice site recognition. In version 3.0, expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors is included. These data are displayed on each intron page for browsing and can be downloaded for other types of analysis.

Proper citation: Yeast Intron Database (RRID:SCR_007144) Copy   

•   Source: SciCrunch Registry

http://kevin-gattaca.blogspot.fr/

A Weblog on Bioinformatics, Genome Science and Next Generation Sequencing.

Proper citation: Kevin's GATTACA World (RRID:SCR_007191) Copy   

•   Source: SciCrunch Registry

https://omictools.com/ecgene-tool

Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns.

Proper citation: ECgene: Gene Modeling with Alternative Splicing (RRID:SCR_007634) Copy   

•   Source: SciCrunch Registry

http://www.transcriptionfactor.org/index.cgi?Home

Database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. The predictions are based on domain assignments from the SUPERFAMILY and Pfam hidden Markov model libraries. Benchmarks of the transcription factor predictions show they are accurate and have wide coverage on a genomic scale. The DBD consists of predicted transcription factor repertoires for 930 completely sequenced genomes.

Proper citation: DBD: Transcription factor prediction database (RRID:SCR_002300) Copy   

•   Source: SciCrunch Registry

http://drtf.cbi.pku.edu.cn/

Database collection of known and predicted transcription factors of Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica. DRTF currently contains 2,025 putative transcription factors (TF) gene models in indica and 2,384 in japonica, distributed in 63 families. THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026.

Proper citation: Database of Rice Transcription Factors (RRID:SCR_002413) Copy   

•   Source: SciCrunch Registry

http://mips.helmholtz-muenchen.de/genre/proj/corum

Database of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, but data from high-throughput experiments is excluded.
The majority of protein complexes in CORUM originates from man (65%), followed by mouse (14%) and rat (14%)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CORUM (RRID:SCR_002254) Copy   

•   Source: SciCrunch Registry

http://genecards.org

Database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. Information featured in GeneCards includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, pathways, protein-protein interactions, related drugs and compounds and direct links to cutting edge research reagents and tools such as antibodies, recombinant proteins, clones, expression assays and RNAi reagents.

Proper citation: GeneCards (RRID:SCR_002773) Copy   

•   Source: SciCrunch Registry

http://www.coryneregnet.de

Reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks. It generates links to genome annotations, to identified transcription factors and to the corresponding cis-regulatory elements. CoryneRegNet is based on a multi-layered, hierarchical and modular concept of transcriptional regulation and was implemented by using the relational database management system MySQL and an ontology-based data structure.

Proper citation: CoryneRegNet (RRID:SCR_002255) Copy   

•   Source: SciCrunch Registry

http://mmonot.eu/COV2HTML/connexion.php

An interactive web interface addressed to biologists, allowing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). Its strength is to make NGS analysis without software installation, login or long training period.

Proper citation: COV2HTML (RRID:SCR_002886) Copy   

•   Source: SciCrunch Registry

http://zfin.org

Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.

Proper citation: Zebrafish Information Network (ZFIN) (RRID:SCR_002560) Copy   

•   Source: SciCrunch Registry

http://phylogenomics.blogspot.fr/

Blog by evolutionary biologist and UC Davis professor Jonathan Eisen. Topics of his posts include microbiology, phylogenomics, product reviews, and a variety of miscellaneous topics.

Proper citation: Tree of Life (RRID:SCR_002436) Copy   

•   Source: SciCrunch Registry

http://t3db.org/

Database that combines detailed toxin data with comprehensive toxin target information. The database currently houses 3,053 toxins described by 32,276 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to 1,670 corresponding toxin target records. Altogether there are 37,084 toxin, toxin target associations. (March 2014) Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. This information has been extracted from over 5,454 sources sources, which include other databases, government documents, books, and scientific literature. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure, and relational query searches

Proper citation: T3DB (RRID:SCR_002672) Copy   

•   Source: SciCrunch Registry

http://ecocyc.org/

Database for the bacterium Escherichia coli K-12 MG1655, the EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways. The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms.

Proper citation: EcoCyc (RRID:SCR_002433) Copy   

•   Source: SciCrunch Registry

http://mint.bio.uniroma2.it/domino/

Open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains. The curation effort aims at covering the interactions mediated by the following domains (SH3, SH2, 14-3-3, PDZ, PTB, WW, EVH, VHS, FHA, EH, FF, BRCT, Bromo, Chromo, GYF). The interactions deposited in DOMINO are annotated according to the PSI MI standard and can be easily analyzed in the context of the global protein interaction network as downloaded from major interaction databases like MINT, INTACT, DIP, MIPS/MPACT. It can be searched with a versatile search tool and the interaction networks can be visualized with a convenient graphic display applet that explicitly identifies the domains/sites involved in the interactions.

Proper citation: DOMINO: Domain peptide interactions (RRID:SCR_002392) Copy   

•   Source: SciCrunch Registry

http://www.drugbank.ca/

Bioinformatics and cheminformatics database that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.

Proper citation: DrugBank (RRID:SCR_002700) Copy   

•   Source: SciCrunch Registry

https://epd.expasy.org/epd/

EPDnew databases are the result of merging Eukaryotic Promoter Database, EPD, promoters within house analysis of promoter specific high throughput data for selected organisms only. EPDnew is a set of species specific databases of experimentally validated promoters.

Proper citation: EPDnew (RRID:SCR_002485) Copy   

•   Source: SciCrunch Registry

http://hint.yulab.org/

A database of high-quality protein-protein interactions in different organisms.

Proper citation: HINT (RRID:SCR_002762) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/gene

Database for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available.

Proper citation: Entrez Gene (RRID:SCR_002473) Copy   

•   Source: SciCrunch Registry