Tools   Select Another Resource Report Type

http://itfp.biosino.org/itfp/

ITFP is an integrated transcription factor (TF) platform, which included abundant TFs and targets message of mammalian. Support vector machine (SVM) algorithm combined with error-correcting output coding (ECOC) algorithm was utilized to identify and classify transcription factor from protein sequence of Human, Mouse and Rat. For transcription factor targets, a reverse engineering method named ARACNE was used to derive potential interaction pairs between transcription factor and downstream regulated gene from Human, Mouse and Rat gene expression profile data. Detailed information of gene expression profile data can be found in help page. Moreover, all data provided by the platform is free for non-commercial users and can be downloaded through links on help page.

Proper citation: Intergrated Transcription Factor Platform (RRID:SCR_008119) Copy   

•   Source: SciCrunch Registry

http://wodaklab.org/iRefWeb/

iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from nine different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. Integration is achieved through a rigorously documented procedure for mapping protein IDs across databases, enabling systematic backtracking of the links used to establish the identity of the interaction partners. The iRefWeb interface groups interaction records from the different databases into a single non-redundant view. In particular iRefWeb facilitates comparing interaction records as seen by the various source databases relative to the PubMeds they were annotated from. iRefWeb is one of several views of the iRefIndex resource. Data are also available in a tab-delimited plain-text format (PSI-MITAB) as well as planned releases of a PSI-XML formatted version and a Cytoscape plugin. Further details about the iRefIndex project as well as data downloads are available from here . The method used to build iRefIndex is described in a recent publication.

Proper citation: Interaction Reference Index Web Interface (RRID:SCR_008118) Copy   

•   Source: SciCrunch Registry

http://pbil.univ-lyon1.fr/databases/homolens.php

Database of homologous genes from Ensembl organisms, structured under ACNUC sequence database management system. It allows to select sets of homologous genes among species, and to visualize multiple alignments and phylogenetic trees. It is possible to search for orthologous genes in a wide range of taxons. HOMOLENS is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generally, HOMOLENS gives an overall view of what is known about a peculiar gene family. Note that HOMOLENS is split into two databases on this server: HOMOLENS contains the protein sequences while HOMOLENSDNA contains the nucleotide sequences. Protein sequences of HOMOLENS have been generated by translating the CDS of HOMOLENSDNA and using associated cross-references to generate the annotations.

Proper citation: Homologous Sequences in Ensembl Animal Genomes (RRID:SCR_008356) Copy   

•   Source: SciCrunch Registry

http://www.ingenuity.com/

A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base .

Proper citation: Ingenuity Pathways Knowledge Base (RRID:SCR_008117) Copy   

•   Source: SciCrunch Registry

http://nesg.org:9090/HCPIN/

The Human Cancer Pathway Protein Interaction Network (HCPIN) was constructed as a step toward better integrating protein three-dimensional (3D) structural information in cancer systems biology. It was constructed by analysis of several classical cancer-associated signaling pathways and their physical protein-protein interactions. The HCPIN Website provides a comprehensive description of this biomedically important multipathway network together with experimental and homology models of HCPIN proteins useful for cancer biology research.

Proper citation: Human Cancer Protein Interaction Network (RRID:SCR_008116) Copy   

•   Source: SciCrunch Registry

http://www.primervfx.com/#welcome

PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome. Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs. -There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names) -you can use genome regions (chromosome coordinates, chromosome bands if exists) -Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers -euPCR for eukaryotic organisms genes/exons primers -snpPCR for eukaryotic organisms SNP primers Sponsors: PrimerStudio is funded by the University of Tartu.

Proper citation: PrimerStudio (RRID:SCR_008232) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics2.wsu.edu/cgi-bin/Athena/cgi/home.pl

Athena is a web-based application that warehouses disparate datatypes related to the control of gene expression. Athena provides several features to enable exploration of the regulatory mechanisms of Arabidopsis gene control. The first main tool we provide is visualization of promoter domains of selected genes. Database crossreference for these transcription factors is provided as well as a statistical test for enrichment of binding activity within the set of selected promoters. The data mining tools in Athena allow for selection of sets of genes based on two different factors. -Genes can be select by specifying a set of binding factors whose putative sites must be present within all of those genes'' promoter regions. -Alternatively, genes can be selected using Gene Ontology annotations. Both GO (Gene Ontology) Slim terms and Gene Ontology terms are available. One can select a set of genes by either choosing a union of the genes annotated by a selected set of Slim terms or Gene Ontology terms. The selected gene''s putative binding factors are listed, including enrichment data. Furthermore, enriched presence of Gene Ontology terms is given. The analysis suite provides both enhanced data mining tools for selecting genes as well as several data displays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Athena (RRID:SCR_008110) Copy   

•   Source: SciCrunch Registry

http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?iter

ITER is a toxicology data file on the National Library of Medicine''s (NLM) Toxicology Data Network. It contains data in support of human health risk assessments. It is compiled by Toxicology Excellence for Risk Assessment (TERA) and contains over 600 chemical records with key data from the Agency for Toxic Substances & Disease Registry (ATSDR), Health Canada, National Institute of Public Health & the Environment (RIVM) - The Netherlands, U.S. Environmental Protection Agency (EPA), and independent parties whose risk values have undergone peer review. ITER provides a comparison of international risk assessment information in a side-by-side format and explains differences in risk values derived by different organizations. ITER data, focusing on hazard identification and dose-response assessment, is extracted from each agencys assessment and contains links to the source documentation. Among the key data provided in ITER are ATSDRs minimal risk levels; Health Canadas tolerable intakes/concentrations and tumorigenic doses/concentrations; EPAs carcinogen classifications, unit risks, slope factors, oral reference doses, and inhalation reference concentrations; RIVMs maximum permissible risk levels; NSF International''s reference doses and carcinogen risk levels, IARC''s cancer classifications, and noncancer and/or cancer risk values (that have undergone peer review) derived by independent parties. Users can search by chemical or other name, chemical name fragment, or Chemical Abstracts Service Registry Number(RN), and/or subject terms. Search results can easily be viewed, printed or downloaded. Search results are displayed in relevancy ranked order. Users may select to display exact term matches, complete records, or any combination of data from the following broad groupings: -Noncancer Oral -Cancer Oral -Noncancer Inhalation -Cancer Inhalation

Proper citation: International Toxicity Estimates for Risk (RRID:SCR_008196) Copy   

•   Source: SciCrunch Registry

http://www.jenner.ac.uk/

JenPep is a database of quantitative binding data for immunological protein-peptide interactions. It is a system which allows speedy access to this binding data through simple on-line interfaces and effective search mechanisms.

Proper citation: JenPep (RRID:SCR_008191) Copy   

•   Source: SciCrunch Registry

http://www.thearkdb.org/arkdb/

This website contains the mapping sequence of poultry. The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal species. In doing so, it aims to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data. It's supported, in part, by the USDA-CSREES National Animal Genome Research Program in order to serve the poultry genome mapping community. This system represents a complete rewrite of the original version with the code migrated to java and the underlying database targeted at postgres (although any standards-compliant database engine should suffice). The initial release records details of maps and the markers that they contain. There are alternative entry points that target either a chromosome or a specific mapping analysis as the starting point. Limited relationships between markers are recorded and displayed. As with the previous version, all maps are drawn using data extracted from the database on the fly.

Proper citation: ChickBase (RRID:SCR_008147) Copy   

•   Source: SciCrunch Registry

http://microbialgenomics.energy.gov/index.shtml

Through its Microbial Genome Program (MGP) and its Genomics:GTL (GTL) program, DOEs Office of Biological and Environmental Research (BER) has sequenced more than 485 microbial genomes and 30 microbial communities having specialized biological capabilities. Identifying these genes will help investigators discern how gene activities in whole living systems are orchestrated to solve myriad life challenges. The MGP was begun in 1994 as a spinoff from the Human Genome Program. The goal of the program was to sequence the genomes of a number of nonpathogenic microbes that would be useful in solving DOE''s mission challenges in environmental-waste cleanup, energy production, carbon cycling, and biotechnology. Past projects include microbial genome program, microbial cell project, and the Laboratory Science Program at the DOE Joint Genome Institute. The two ongoing projects are Genomics: GTL program and Community Sequencing Program at the DOE Joint Genome Institute. Sponsors: Site sponsored by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Microbial Genomics Program (RRID:SCR_008140) Copy   

•   Source: SciCrunch Registry

http://www.biology.emory.edu/research/Prinz/database/database.html

This page describes the contents of a database of 1.7 million model neurons. This database is available for interested researchers after contacting the creators, but is not web accessible. The construction and analysis of the database are described in detail in Prinz AA, Billimoria CP, Marder E (2003). Alternative to hand-tuning conductance-based models: construction and analysis of databases of model neurons. J Neurophysiol 90: 3998-4015. Because of its size (over 6 GB even in the zipped version), it is not practicable to download the database over the internet. Instead, we have made multiple copies of the database on sets of two DVDs each. We are happy to send a set of DVDs to anybody who is interested upon e-mail request to Astrid Prinz.

Proper citation: Crustacean stomatogastric model neuron database (RRID:SCR_008260) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/ipd/mhc/bola/

This website is intended to be the definitive source of information on the bovine major histocompatibility complex - its genes, proteins and polymorphism. Its purpose is to collate data on the Bovine Leucocyte Antigens (BoLA) and provide a forum for the analysis and nomenclature of polymorphisms in the genes and proteins of the bovine MHC. The BoLA nomenclature committee is a standing committee of the International Society for Animal Genetics. Its purpose is to collate data on the Bovine Leucocyte Antigens (BoLA) and provide a forum for the analysis and nomenclature of polymorphisms in the genes and proteins of the bovine MHC. The information gathered here is based on the BoLA workshop reports, which are published in Animal Genetics and the European Journal of Immunogenetics. The workshop report data are reproduced with the permission of the publishers Blackwell Science, and other text on the site is used with the permission of CRC Press.

Proper citation: BoLA Nomenclature: International Society for Animal Genetics (RRID:SCR_008142) Copy   

•   Source: SciCrunch Registry

http://www.who.int/gho/en/

WHOSIS, the WHO Statistical Information System, is an interactive database bringing together core health statistics for the 193 WHO Member States. It comprises more than 100 indicators, which can be accessed by way of a quick search, by major categories, or through user-defined tables. The data can be further filtered, tabulated, charted and downloaded. The data are also published annually in the World Health Statistics Report released in May. The WHO Statistical Information System is the guide to health and health-related epidemiological and statistical information available from the World Health Organization. Most WHO technical programs make statistical information available, and they will be linked from here. Sponsors: WHOSIS is supported by the World Health Organization. Note: The WHO Statistical Information System (WHOSIS) has been incorporated into the Global Health Observatory (GHO) to provide you with more data, more tools, more analysis and more reports.

Proper citation: World Health Organization Statistical Information System (RRID:SCR_008250) Copy   

•   Source: SciCrunch Registry

http://etblast.vbi.vt.edu/argh/index.shtml

ARGH is an automated, accurate and scalable method by which acronym-definition pairs can be identified within text. Its primary advantage is in enabling information processing methods to resolve author-defined acronyms, however it also allows an automated creation of a reference work on acronym definitions.
ARGH has several advantages over manual or semi-automated methods, besides time and effort saved, such as enabling identification of relative frequencies for alternate acronyms and definitions as well as spelling, phrasing and hyphenation variants for a unique acronym-definition pair. It also aids users in identifying acronym/definition variants present in the literature that may not necessarily be in biomedical databases.
ARGH functions by a set of heuristics to accurately locate and identify the boundaries of acronym-definition pairs was developed and refined in terms of precision and recall on subsets of MEDLINE records. These training sets were gradually increased in size and heuristics re-evaluated to ensure scalability.
ARGH can be tested on over 12 million MEDLINE records, and it can identify more than 174,000 unique acronyms and their 737,000 associated definitions. Currently, it is the world''s largest and most comprehensive catalog of biomedical acronyms and abbreviations, containing approximately 257,000 out of an estimated 277,000 unique acronyms within MEDLINE.
Sponsors: ARGH is a service of UT Southwestern eTBLAST team.

Proper citation: ARGH: Biomedical Acronym Resolver (RRID:SCR_008131) Copy   

•   Source: SciCrunch Registry

http://www.pd-doc.org/Databases/LinkedDatabases/PSGDatabases/QE2Study/tabid/160/Default.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. This site has a dataset from the QE2 Study: Effects of CoEnzyme Q10 in Early Parkinson's Disease, was an NINDS funded pilot study of 80 subjects with early untreated Parkinson's disease (PD). The PI was Clifford Shults, MD at UCSD. It was a randomized, double-blind, parallel group comparison of three doses of coenzyme Q10 (CoQ10) (300, 600 and 1200 mg/day) versus placebo in patients and do not yet require treatment with levodopa. The QE2 Study: Effects of CoEnzyme Q10 in Early Parkinson's Disease, was an NINDS funded pilot study of 80 subjects with early untreated Parkinson's disease (PD). The PI was Clifford Shults, MD at UCSD. It was a randomized, double-blind, parallel group comparison of three doses of coenzyme Q10 (300, 600 and 1200 mg/day) versus placebo in patients and do not yet require treatment with levodopa or any other antiparkinsonian medication. Enrollment period May 1999 Feb. 2000; study participation ended June 2001.

Proper citation: Effects of CoEnzyme Q10 in Early Parkinson's Disease (RRID:SCR_008094) Copy   

•   Source: SciCrunch Registry

http://mips.gsf.de/proj/ppi/

The MIPS mammalian protein-protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals. The content is based on published experimental evidence that has been processed by human expert curators. It is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions. To suit different users needs we provide a variety of interfaces to search the database: -Expert interface Simple but powerful boolean query language. -PPI search form Easy to use PPI search -Protein search Just find proteins of interest in the database Sponsors: This work is funded by a grant from the German Federal Ministry of Education and Research.

Proper citation: MIPS Mammalian Protein-Protein Interaction Database (RRID:SCR_008207) Copy   

•   Source: SciCrunch Registry

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

A database of manually annotated mammalian protein complexes. To obtain a high-quality dataset, information was extracted from individual experiments described in the scientific literature. Data from high-throughput experiments was not included.

Proper citation: Mammalian Protein Complex Data Base (RRID:SCR_008209) Copy   

•   Source: SciCrunch Registry

http://pbs.jhu.edu/research/Yantis/publications/ClassicPapers

This website contains a list of classic articles in visual perception. They are listed alphabetically by the last name if the article''s author.

Proper citation: Classic Articles in Visual Perception (RRID:SCR_008325) Copy   

•   Source: SciCrunch Registry

http://skonops.imbb.forth.gr/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 22, 2023. A database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world''''s most important malaria vector. AnoBase is an integrated, relational database of basic biological and genetic data on anopheline species, with a particular emphasis on Anopheles gambiae. It has been designed as an information source and research support tool for the broad vector biology community. Although AnoBase is not a primary genomic database that develops and provides tools to access the genome of the malaria mosquito, it nevertheless contains several sections that offer data of genomic interest such as in situ hybridization images, an integrated gene tool and direct online access to AnoXcel, the proteomic database of An. gambiae. Moreover, AnoBase also contains information on non-gambiae mosquito species and a novel section on studies related to insecticide resistance.

Proper citation: AnoBase: An Anopheles database (RRID:SCR_008166) Copy   

•   Source: SciCrunch Registry