Databases

This section contains databases of coding/non-coding DNA, nucleic acid and gene structure, transcriptional regulator sites, transcription factors, molecular probes, and primers.

Found 77 links

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3D-FootprintDatabase Content

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3D-footprint provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Comparisons with expert-curated databases RegulonDB and TRANSFAC support the quality of structure-based estimates of specificity.

This content is being maintained by brunocontreras.

3DNALandscapesDatabase Content

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3DNALandscapes is a database for exploring the conformational features of DNA. 3DNALandscapes enables searches of conformational information across multiple structures. The database contains a wide variety of structural parameters and molecular images, computed with the 3DNA software package and known to be useful for characterizing and understanding the sequence-dependent spatial arrangements of the DNA sugar-phosphate backbone, sugar-base side groups, base pairs, base-pair steps, groove structure, etc. The data comprise all DNA-containing structures--both free and bound to proteins, drugs and other ligands--currently available in the Protein Data Bank.

ACLAMEDatabase Content

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The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). Classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs.

ADHDgeneDatabase Content

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Genetic database for attention deficit hyperactivity disorder. ADHDgene database was developed by integrating ADHD-related genetic factors by profound literature reading.

Animal Transcription Factor DatabaseDatabase Content

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Comprehensive TF database; identified and classified all the genome-wide TFs in 50 sequenced animal genomes. Also collects transcription co-factors and chromatin remodeling factors of those genomes, which are also essential in the gene transcription regulation.

BioProjectDatabase Content

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A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project.

BioSampleDatabase Content

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The BioSample database contains descriptions of biological source materials used in experimental assays.

BioSample DatabaseDatabase Content

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The BioSample Database at the EBI is designed to hold information about biological samples, particularly samples referenced from other EBI databases. BioSD data will be exchanged with NCBI

CADgeneDatabase Content

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The CADgene, a comprehensive manually curated database for coronary artery disease genes. Candidate genes are classified into 12 functional categories based on their roles in CAD. Each gene includes detailed information from related studies (e.g. the size of case-control, population, SNP, odds ratio, P-value, etc.) and useful annotations, which include general gene information, Gene Ontology annotations, KEGG pathways, protein-protein interactions and others.

CCDBDatabase Content

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The Cervical Cancer gene DataBase (CCDB) is a manually curated catalog of experimentally validated genes that are thought, or are known to be involved in the different stages of cervical carcinogenesis. Each record contains details related to gene like architecture (exon-intron structure), location, function, sequences (mRNA/CDS/protein), ontology, interacting partners, homology to other eukaryotic genomes, structure and links to other public databases, thus augmenting CCDB with external data. Also, manually curated literature references have been provided to support the inclusion of the gene in the database and establish its association with cervix cancer. In addition, CCDB provides information on microRNA altered in cervical cancer as well as search facility for querying, several browse options and an online tool for sequence similarity search.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
CCDB: a curated database of genes involved in cervix cancer20115

CellBaseTool Content

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CellBase is a relational database that contains relevant biological information about genomic features and proteins, gene expression regulation, functional annotation, genomic variation and systems biology information. Integrated are the most relevant repositories such as Ensembl, Uniprot, Omim, COSMIC, IntAct, HapMap, Reactome, and others.

This content is being maintained by imedina.

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ChimerDBDatabase Content

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ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman's database. A new algorithm that is more sensitive, has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Results from the analysis of next-generation sequencing data in the short read archives are incorporated along with a new alignment viewer.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
ChimerDB 2.0--a knowledgebase for fusion genes updated20106

CIViC - Clinical Interpretation of Variants in CancerResource Content

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Precision medicine refers to the use of prevention and treatment strategies that are tailored to the unique features of each individual and their disease. In the context of cancer this might involve the identification of specific mutations shown to predict response to a targeted therapy. The biomedical literature describing these associations is large and growing rapidly. Realizing precision medicine will require this information to be centralized, debated and interpreted for application in the

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COSMICDatabase Content

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COSMIC curates comprehensive information on somatic mutations in human cancer. Release v48 (July 2010) describes over 136,000 coding mutations in almost 542,000 tumour samples; of the 18,490 genes documented, 4803 (26%) have one or more mutations. Full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs. Biomart allows more automated data mining and integration with other biological databases. Annotation of genomic features has become a significant focus. COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources.

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