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Databases

This section contains human genome and ORFs, genetics, polymorphism, gene-/system-/disease-specific information.

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Allele frequency netDatabase Content

http://www.allelefrequencies.net

Human Genome > Databases

The allele frequency net database is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. At present, the system contains data on the frequency of genes from different polymorphic regions such as human leukocyte antigens, killer-cell immunoglobulin-like receptors, major histocompatibility complex Class I chain-related genes and a number of cytokine gene polymorphisms.

NAR Database Issue 2011
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tagscytokines gene frequency genotype haplotypes histocompatibility antigens class i humans kir receptors major histocompatibility complex nucleic acid databases

AntigenDBDatabase Content

http://www.imtech.res.in/raghava/antigendb/

Human Genome > Databases

AntigenDB contains 500 antigens to pathogenic species curated from the literature and other immunological resources. In AntigenDB, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with additional information such as B and T-cell epitopes, MHC binding, function, gene-expression and post translational modifications, where available. AntigenDB also provides links to major internal and external databases.

This content is being maintained by raghavagps.

NAR Database Issue 2010
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tagsantigens communicable diseases computational biology epitopes genetic databases humans immune system immunogenetics lymphocytes peptide mapping post-translational protein processing protein databases tertiary protein structure

ASPicDBDatabase Content

http://www.caspur.it/ASPicDB/

Human Genome > Databases
Protein > Databases

ASPicDB provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user.

This content is being maintained by Graziano Pesole.

NAR Database Issue 2011
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tagsalternative splicing exons genetic databases genetic variation humans messenger rna protein isoforms protein sequence analysis proteins

ConsensusPathDBDatabase Content

http://cpdb.molgen.mpg.de

Human Genome > Databases
Model Organisms > Databases
Protein > Databases

ConsensusPathDB is a meta-database that integrates physical protein interactions, metabolic and signaling reactions and gene regulatory interactions in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. ConsensusPathDB offers different ways of utilizing these integrated interaction data, with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways.

NAR Database Issue 2011
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tagsanimals factual databases gene expression gene regulatory networks genetic databases humans metabolic networks and pathways mice protein interaction mapping signal transduction

COSMICDatabase Content

http://www.sanger.ac.uk/genetics/CGP/cosmic/

DNA > Databases
Human Genome > Databases

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.

NAR Database Issue 2010NAR Database Issue 2011
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tagscomputational biology data mining genetic databases human genome humans mutation neoplasms nucleic acid databases protein databases search engine tumor cell line

dbDEPCDatabase Content

http://lifecenter.sgst.cn/dbdepc/index.do

Human Genome > Databases
Protein > Databases

A database of differentially expressed proteins in human cancers (dbDEPC) collects curated cancer proteomics data, provides a resource for information on protein-level expression changes, and explores protein profile differences among different cancers. dbDEPC currently contains 1803 proteins differentially expressed in 15 cancers, curated from 65 mass spectrometry (MS) experiments in peer-reviewed publications.

NAR Database Issue 2010
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tagscomputational biology dna gene expression profiling genetic databases human genome humans neoplasms neoplastic gene expression regulation protein databases proteome rna

FANTOMDatabase Content

http://fantom.gsc.riken.jp/4/

Expression > Databases
Human Genome > Databases

The Functional Annotation Of the Mammalian Genome (FANTOM) is a database for the transcriptional network that regulates macrophage differentiation. Data comes from cap analysis of gene expression (CAGE), sequencing mRNA 5'-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP-chip for epigenetic marks and transcription factors.

NAR Database Issue 2011
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tagsanimals cell differentiation gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic transcription genomics humans macrophages mice molecular sequence annotation transcription factors tumor cell line

FINDbaseDatabase Content

http://www.findbase.org

Human Genome > Databases

Frequency of INherited Disorders database (FIND base) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. Other features include: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for markers in genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics journal.

NAR Database Issue 2011
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tagsethnic groups gene frequency genetic markers genetic variation humans inborn genetic diseases nucleic acid databases periodicals as topic pharmacogenetics

Gene WikiDatabase Content

http://en.wikipedia.org/wiki/Portal:Gene_Wiki

Human Genome > Databases

The Gene Wiki goal is to build a gene-specific review article for every gene in the human genome, where each article is collaboratively written, continuously updated and community reviewed. Gene Wiki articles are freely accessible within the Wikipedia web site.

NAR Database Issue 2010
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tagscomputational biology genetic databases genetic models genetics humans nucleic acid databases protein databases protein interaction mapping

H-InvDBDatabase Content

http://www.h-invitational.jp/

Human Genome > Databases

The H-Invitational Database (H-InvDB) is a comprehensive annotation resource of human genes and transcripts. The latest release of H-InvDB (release 6.2) provides the annotation for 219,765 human transcripts in 43,159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources-'Navigation search', 'H-InvDB Enrichment Analysis Tool (HEAT)' and web service APIs.

This content is being maintained by cyamasak.

NAR Database Issue 2010
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tagsalternative splicing complementary dna computational biology genes genetic databases genetic models genetic polymorphism human genome humans messenger rna microsatellite repeats multigene family nucleic acid databases oligonucleotide array sequence analysis open reading frames single nucleotide polymorphism tertiary protein structure

HLungDBDatabase Content

http://www.megabionet.org/bio/hlung/

Human Genome > Databases

The human lung cancer database (HLungDB) is a database with the integration of the lung cancer-related genes, proteins and miRNAs together with the corresponding clinical information. Currently, we have collected 2585 genes and 212 miRNA with the experimental evidences involved in the different stages of lung carcinogenesis through text mining. The results from analysis of transcription factor-binding motifs, the promoters and the SNP sites for each gene are also included. Genes with epigenetic regulation were also included.

NAR Database Issue 2010
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tagsamino acid motifs computational biology gene regulatory networks genetic databases genetic epigenesis humans lung neoplasms micrornas neoplastic cell transformation nucleic acid databases protein databases transcription factors

HRTBLDbDatabase Content

http://motif.bmi.ohio-state.edu/hrtbldb/

Human Genome > Databases

The Hormone Receptor Target Binding Loci, HRTBLDb database contains hormone receptor binding regions (binding loci) from in vivo ChIP-based high-throughput experiments as well as in silico, computationally predicted, binding motifs and cis-regulatory modules for the co-occurring transcription factor binding motifs, which are within a binding locus. It also contains individual binding sites whose regulatory action has been verified by in vitro experiments.

This content is being maintained by vjin.

NAR Database Issue 2010
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tagsamino acid motifs androgen receptors animals computational biology estrogen receptors genetic databases humans nucleic acid databases protein binding protein databases tertiary protein structure thyroid hormone receptors

IGDDDatabase Content

http://www.igdd.iicb.res.in

DNA > Databases
Human Genome > Databases

Indian Genetic Disease Database (IGDD) is an integrated and curated repository of mutation data on common genetic diseases afflicting the Indian populations. Information on locus heterogeneity, type of mutation, clinical and biochemical data, geographical location and common mutations are furnished based on published literature. The database can be searched based on disease of interest, causal gene, type of mutation and geographical location of the patients or carriers.

NAR Database Issue 2011
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tagseuropean continental ancestry group humans inborn genetic diseases india mutation nucleic acid databases

IMGT/HLA databaseDatabase Content

http://www.ebi.ac.uk/imgt/hla/

Human Genome > Databases

The IMGT/HLA database provides a searchable repository of highly curated HLA sequences. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data.

NAR Database Issue 2011
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tagsalleles hla antigens humans protein databases terminology as topic

Immune Epitope DatabaseDatabase Content

http://tools.immuneepitope.org/

Human Genome > Databases
Protein > Databases

The Immune Epitope Database (IEDB) provides a catalog of experimentally characterized B and T cell epitopes, as well as data on Major Histocompatibility Complex (MHC) binding and MHC ligand elution experiments. The database represents the molecular structures recognized by adaptive immune receptors and the experimental contexts in which these molecules were determined to be immune epitopes. Epitopes recognized in humans, nonhuman primates, rodents, pigs, cats and all other tested species are included. Both positive and negative experimental results are captured. The database can be queried by epitope structure, source organism, MHC restriction, assay type or host organism, among other criteria.

NAR Database Issue 2010
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tagsanimals communicable diseases computational biology epitopes genetic databases humans immune system immunogenetics major histocompatibility complex peptides protein databases proteins

Tags associated with subcategory 'Human Genome/Databases'

humans genetic databases nucleic acid databases computational biology protein databases animals tertiary protein structure plant genome protein binding neoplasm genes mutation thyroid hormone receptors peptides gene regulatory networks genetic epigenesis neoplastic gene expression regulation rna neoplasms human genome lung neoplasms neoplastic cell transformation transcription factors estrogen receptors peptide mapping base sequence dna repair polymerase chain reaction dna primers post-translational protein processing lymphocytes immune system microsatellite instability epitopes communicable diseases gene expression regulation androgen receptors microsatellite repeats molecular sequence data immunogenetics micrornas gene silencing controlled vocabulary database management systems sequence homology viral genome systems integration united states documentation genes signal transduction statistical data interpretation sequence analysis proteome hippocampus natural language processing proteins phylogeny nucleic acids genetics protein interaction mapping genetic models single nucleotide polymorphism mice up-regulation quantitative trait loci genetic variation genome European Bioinformatics Institute (EBI) gene expression profiling europe phenotype genomics invertebrates molecular models major histocompatibility complex nucleic acid sequence homology protein sequence analysis cytokines disease amino acid repetitive sequences protein isoforms catalytic domain ligands genotype haplotypes cell differentiation genetic transcription metabolic networks and pathways terminology as topic histocompatibility antigens class i kir receptors hla antigens exons nucleic acid hybridization genetic predisposition to disease genome-wide association study bacterial genome data mining dna fungal genome biological processes