Curator Dashboard

CellCircuits is an open-access database of molecular network models. Its goal is to bridges the gap between databases of individual pair-wise molecular interactions and databases of validated pathways. It contains functional network hypotheses produced by algorithms that screen molecular interaction networks based on their correspondence with expression or phenotypic data, their internal structure, or their conservation across species. The database is searchable using protein/gene names and Gene Ontology terms. Models are available either as images or in machine-readable formats. Overall, this resource serves as a clearinghouse in which theorists may distribute or revise models in need of validation and experimentalists may search for models or specific hypotheses relevant to their interests. Funding provided by the National Science Foundation (NSF 0425926).

• Resource
• SciCrunch
• 17 years ago - by Anonymous

CE is a databases of alignments for all polypeptide chains. A representative set of proteins is available and kept current with the PDB, a method for calculating pairwise structure alignments. CE aligns two polypeptide chains using characteristics of their local geometry as defined by vectors between C alpha positions. Matches are termed aligned fragment pairs (AFPs). Heuristics are used in defining a set of optimal paths joining AFPs with gaps as needed. The path with the best RMSD is subject to dynamic programming to achieve an optimal alignment. For specific families of proteins additional characteristics are used to weight the alignment. Complete details are described in the paper (PDF format). Databases of alignments for all polypeptide chains and a representative set of proteins is available and kept current with the PDB

• Resource
• SciCrunch
• 17 years ago - by Anonymous

An ontology that describes the Congenital Heart Defects data.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels: Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis Users can search CATH by ID/Sequence/text. They can also browse CATH from the top of the hierarchy, or download CATH data.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

CATdb collects together all the information on transcriptome experiments done at URGV with CATMA micro arrays. All data in CATdb come from the URGV micro array platforms. Common procedures are used including any steps from the experiment design to the statistical analyses. Directed through a WEB interface, biologists enter the standard description of each experimental step (extraction, labelling, hybridization and scanning). Then, normalization and statistical analyses are done following a set of selected methods depending on the experimental design and array types.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

CASRdb is a calcium-sensing receptor locus-specific database for mutations causing familial (benign) hypocalciuric hypercalcemia, neonatal severe hyperparathyroidism, and autosomal dominant hypocalcemia. The information can be searched by mutation, genotype-phenotype, clinical data, in vitro analyses, and authors of publications describing the mutations. CASRdb is regularly updated for new mutations and it also provides a mutation submission form to ensure up-to-date information. The home page of this database provides links to different web pages that are relevant to the CASR, as well as disease clinical pages, sequence of the CASR gene exons, and position of mutations in the CASR. The CASRdb will help researchers to better understand and analyze the mutations, and aid in structure-function analyses.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

CarpeDB is a database focused on epilepsy genetics. It serves as a novel source for epilepsy researchers by featuring scores of epilepsy genes and associated publications in one locus. Furthermore, because multiple genes implicated in epilepsy are also implicated in other human disorders, the use of CarpeDB need not be limited to epilepsy researchers. Users can search the data in Carpe DB by chromosome, gene, species, or keyword. They can also browse genes by an alphabetical list. The website also provides links to other epilespy-related resources, and the ability for users to submit their own data or papers.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

CandidaDB is a database dedicated to the analysis of the genome of the human fungal pathogen, Candida albicans. Its purpose is to collate and integrate various aspects of the genomic information from C. albicans, which is currently responsible for the vast majority of life-threatening fungal infections in immuno-compromized individuals. CandidaDB provides an almost complete dataset of DNA and protein sequences derived from C. albicans strain SC5314, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). Nucleotide sequence data for C. albicans were obtained from the Stanford Genome Technology Center website. Sequencing of C. albicans was accomplished with the support of the NIDR and the Burroughs Wellcome Fund. CandidaDB is supplemented with information from C. albicans entries present in the EMBL/GenBank/DDBJ databanks, as well as observations either published in international journals or communicated directly to us by individual researchers.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A database of Arabidopsis Gene-specific Sequence Tags (GSTs) designed and produced by the CATMA consortium. The aim of CATMA is the design and production of high quality GSTs covering most Arabidopsis genes. The GST repertoire is used by numerous groups for the production of DNA arrays for transcript profiling experiments.The database contains information about the GST probes, the PCR primers used for their amplification and the genes to which they hybridize, together with other information such as details of the groups involved and quality control results. CATMA microarrays constitute the foundation of the CAGE project aiming at the construction of a gene expression reference database for Arabidopsis. The CATMA GSTs are also the basic materials in the AGRIKOLA project focusing on the large-scale systematic RNAi silencing of Arabidopsis genes. CATMA is a consortium of research groups from eight European countries. All CATMA members are public laboratories, some with ties to private research institutions.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2015. The CancerGenes resource simplifies the process of gene selection and prioritization in large collaborative projects. CancerGenes combines gene lists annotated by experts with information from key public databases. Gene lists in the CancerGenes resource are from various sources and have been mapped to UCSC canonical gene IDs. Each gene is annotated with gene name(s), functional description, organism, chromosome number, location, Entrez Gene ID, GO terms, InterPro descriptions, gene structure, protein length, transcript count, and experimentally determined transcript control regions, as well as links to Entrez Gene, COSMIC, and iHOP gene pages and the UCSC and Ensembl genome browsers. The user-friendly interface provides for searching, sorting and intersection of gene lists. Users may view tabulated results through a web browser or may dynamically download them as a spreadsheet table.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application for TDT test on markers with more than two alleles using a logistic regression analysis. (entry from Genetic Analysis Software).

• Resource
• SciCrunch
• 14 years ago - by Anonymous

Cancer Chromosomes is an integration of three databases, the NCI/NCBI SKY/M-FISH & CGH Database, the NCI Mitelman Database of Chromosome Aberrations in Cancer, and the NCI Recurrent Aberrations in Cancer, which all focus on various aspects of cancer and cancer genes. The goal of the SKY/M-FISH and CGH database is to provide a public platform for investigators to share and compare their molecular cytogenetic data. The database is open to everyone and all users can view an individual investigator''s public data or compare public cases from different investigators. The information in the Mitelman Database of Chromosome Aberrations in Cancer relates chromosomal aberrations to tumor characteristics, based either on individual cases or associations. All the data have been manually culled from the literature. Complete karyotypes, patient characteristics, and references are found in the Mitelman Database of Chromosome Aberrations in Cancer. Users can search all three databases for cytogenetic, clinical, and/or reference information.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Expression profiling and promoter identification software tool for transcriptional network analysis and transcriptome characterization. DeepCAGE, the combination of next-generation sequencing with next generation expression profiling provides unsurpassed solutions for expression profiling and genome annotation. CAGE will be the experimental approach at need to link gene expression and control regions in the genome. With the availability of next-generation sequencing methods, DNAFORM now offers DeepCAGE services. DeepCAGE libraries are prepared for direct analysis by an Illumina/Solexa Sequencer. One sequencing run using one channel on an Illumina/Solexa Sequencer can yield in over 4,000,000 reads per sample. CAGE is based on our full-length cDNA library technology, where an adaptor is ligated to the 5''''-end of full-length cDNAs, which introduces a recognition site for a Class IIs restriction endonuclease adjacent to the 5''''-end of the cDNA. The Class IIs restriction endonuclease, here MmeI, allows for the cloning of short tags as derived from the 5''''-end of transcripts into concatemers for high-throughput sequencing. CAGE tags are further characterized by mapping to genomic sequences, which enables the identification of transcriptional start sites. As such CAGE can contribute to projects in Gene Discovery, Gene Expression, and Promoter Identification. After the genome sequencing projects have provided us with the genetic blueprints for many organisms, new questions have to be answered on how to correlate the observed genotypes with related phenotypes, and how to understand the regulation of genetic information in time and space. The dynamics of living systems and the functional behavior of cells in multicellular organisms has thus become the subject of the emerging field of system biology. Integration of experimental approaches and computer aided theories on a system level will be the fundamental principle to drive systems biology in order to understand the principles behind complex regulatory networks, which will be an ambitious goal requiring new approaches in life sciences. For ordering and additional information, please contact us under contact_at_dnaform.jp

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Conformation Angles DataBase is a comprehensive, authoritative and timely knowledge base developed to facilitate retrieval of information related to the conformational angles (main-chain and side-chain) of the amino acid residues present in the non-redundant (both 25% and 90%) data set. The database includes the options of determining the dependency of the conformation angles of a particular residue upon the flanking residues in main-chain, doublet analysis, triplet analysis and analysis of a particular protein structure. It is worth mentioning that for all the options, a user-friendly and convenient Java Graphical User Interface (GUI) has been provided to display the output on the client machine.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

BuchneraBase is a database designed to encapsulate and reference information obtained from the complete genome sequence of the gamma-proteobacterium Buchnera sp. APS. We have derived a high quality gene and functional annotation for Buchnera sp. APS. BuchneraBASE also provides for cross-referencing to the genomes of six further symbiotic bacteria for which full sequences are now available: Buchnera sp. SG from the aphid Schizaphis graminum, Buchnera sp. Bp from the aphid Baizongia pistacea, Wigglesworthia glossinidia brevipalpis from the tetse fly Glossina brevipalpis, Blochmannia floridanus from the carpenter ant Camponotus floridanus, Blochmannia pennsylvanicus from the carpenter ant, Camponotus pennsylvanicus, and Baumannia cicadellinicola from the glassy winged sharpshooter, Homalodisca coagulata. We also include Mycoplasma genitalium, with the smallest genome of an organism that can be grown in pure culture. We have constructed BuchneraBASE to facilitate the post-genomic analysis of these bacteria, especially the genomic correlates of co-operative intracellular lifestyles.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Software application that tests for association between genetic marker and disease by examining the transmission of markers from parents to affected offspring. The main features which differ from other similar programs are: (1) It can deal with transmission of multi-locus haplotypes, even if phase is unknown, and (2) Parental genotypes may be unknown. (entry from Genetic Analysis Software)

• Resource
• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.BSD is a database resource that provides information on strains of bacteria with biodegradative properties. The goal of the database is to consolidate and provide rapid access to comparative data on known biodegradative microorganisms and the hazardous substances they degrade as a readily accessible resource for researchers and field practitioners. The database also aims to: # facilitate comparative analyses and highlight deficiencies in our current knowledge base # provide corresponding microbiological data to complement and integrate with the chemical and metabolic data of the University of Minnesota Biocatalysis/ Biodegradation Database and the phylogenetic data of the Ribosome Database Project (RDP-II) # to organize strain data and analyze biocatalysis and biodegradation within a phylogenetic perspective # provide database users a forum for input and contribution and correction of data # serve as a model for the presentation of strain-level, microbial data on the internet To this end, it includes individual data and strain pages, search capabilities, and user input functionality., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

CIPRO is an integrated protein database of the ascidian Ciona intestinalis. It has been developed to provide widespread information of the proteins expressed in the ascidian Ciona intestinalis, especially for the researcher who wants to get advanced and useful information for starting biological and biomedical research. The protein information in CIPRO directly links to gene expression, a tool for peptide mass fingerprinting (PMF), intracellular localization, 3D image of early development, and transgenic resources.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

BPS is a database of RNA base pairs with quantitative information on the spatial arrangements of interacting bases, including higher-order base associations, and the context of these interactions in high-resolution crystal structures. The structures are taken from the Nucleic Acid Database (NDB), and the base pairs are identified and characterized with the 3DNA software package. The interactions are classified in terms of residue identities, base-pair positioning, and hydrogen-bonding patterns and related to the structural context in which they occur. A user can browse the atlas of base-pair patterns and carry out searches for patterns of specific types or from specific structures.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Blocks is a database of highly conserved regions of proteins, or Blocks. THe database is no longer maintained or updated and some of its tools are no longer functional. However, Blocks does provide Block Searcher, Get Blocks and Block Maker, aids to detection and verification of protein sequence homology. They compare a protein or DNA sequence to a database of protein blocks (current version), retrieve blocks, and create new blocks, respectively. Users can further view blocks by (keyword or number), search a sequence against the database of blocks, search blocks against each other, or make blocks of their own.

• Resource
• SciCrunch
• 17 years ago - by Anonymous