H-DBAS is a unique database of alternative splicing (AS) based on H-InvDB. The features of H-DBAS is as follows: 1) Representative AS variants (RASVs) were identified from 8 data sets consist of 6 mammalian model organisms (human, mouse, rat, chimpanzee, macaque and dog). The contents of data sets and the corresponding species are as follows: Full-length cDNA data set, mRNA data set, RNA data set 2) Equally-spliced variants (ESVs) were identified from RASVs between human and mouse, rat, chimpanzee, macaque and dog by using comparative genomics. Splice sites and splice motifs affecting SNPs can be observed in human. 3) RASVs affecting protein functions (protein motif, GO, subcellular localization signal and transmembrane domain) can be observed in human. 4) AS junctions expressed in specified cellular fractions (cytoplasm, nuclear and polysome) of human cell were detected by using RNA-Seq tags. The translation validation of the variants having AS junctions were analyzed by compared with RefSeq junctions. The results are shown from RNA-Seq analysis page. ... [Information of the supplier]
The Open Tiger Genome Project is a public service launched by a non-profit foundation Genome Research Foundation (GRF) and TheragenEtex Inc. It is aming at preserving tiger genome information, the level 1 endangered species designated by the Korean Ministry of Environment. Genome Research Foundation is pursuing to complete the standard reference genome of Amur (Korean or Siberian) tiger by sequencing and analyzing its genome. ... [Information of the supplier]
Bgee is a database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization data) on anatomy and development of different species. Then, in order to perform automated cross species comparisons, homology relationships across anatomies, and comparison criteria between developmental stages, are designed. Data can be retrieved by ontology browsing, textual search, expression search, or advanced expression search. Gene expression patterns can be compared by selecting any gene family (e.g. ENSFM00500000270089). The full content of the Bgee expression database, the ontologies, the homology links between anatomical ontologies, and the relationships between developmental ontologies, are all available in the download section. More information is provided in the documentation. All data sources used in Bgee are listed on the data sources page. ... [Information of the supplier]
In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. [Source: http://nar.oxfordjournals.org/content/early/2011/11/15/nar.gkr1007.full] ... [Miscellaneous as indicated]
Cancer GEnome Mine is a public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes. CanGEM supports the MIAME standard and in addition, stores clinical information using standardized controlled vocabularies whenever possible. Microarray probes are re-annotated with their physical coordinates in the human genome and aCGH data is analyzed to yield gene-specific copy numbers. Users can build custom datasets by querying for specific clinical sample characteristics or copy number changes of individual genes. Aberration frequencies can be calculated for these datasets, and the data can be visualized on the human genome map with gene annotations. Furthermore, the original data files are available for more detailed analysis. ... [Information of the supplier, modified]
GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. We actively gather datasets from public domain projects, and encourage direct data submission from the community. GWAS Central is built upon a basal layer of Markers that comprises all known SNPs and other variants from public databases such as dbSNP and the DBGV. Allele and genotype frequency data, plus genetic association significance findings, are added on top of the Marker data, and organised the same way that investigations are reported in typical journal manuscripts. Critically, no individual level genotypes or phenotypes are presented in GWAS Central – only group level aggregated (summary level) data. The largest unit in a data submission is a Study, which can be thought of as being equivalent to one journal article. This may contain one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. Sample Panels may be characterised in terms of various Phenotypes, and they also may be combined and/or split into Assayed Panels. The Assayed Panels are used as the basis for reporting allele/genotype frequencies (in `Genotype Experiments`) and/or genetic association findings (in ‘Analysis Experiments’). Environmental factors are handled as part of the Sample Panel and Assayed Panel data structures. ... [Information of the supplier]
SNPedia is a wiki-based bioinformatics web site that serves as a database of single nucleotide polymorphisms (SNPs). Each article on a SNP provides a short description, links to scientific articles and personal genomics web sites, as well as microarray information about that SNP. [Information of the supplier]
Genetics Home Reference is the National Library of Medicine's Web site for consumer information about genetic conditions and the genes or chromosomes associated with those conditions. You can find Genetic Condition Summaries, Gene Summaries, Gene Family Summaries, Chromosome Summaries, a Handbook and a Glossery on this website. Furthermore there are several learning activities available to help you explore the website and find out about human genetics. ... [Information of the supplier, modified]
This site contains all of the data from our ongoing proteomic analysis of human nucleoli, which is carried out as a collaboration between the Lamond and Mann laboratories (in Denmark and Munich). Using high sensitivity mass spectrometry and stringent criteria, we have so far identified ~700 human nucleolar proteins. More recently, we used a quantitative proteomic approach for the temporal characterization of protein flux through the nucleolus, determining the kinetics of up to 489 nucleolar proteins after various drug treatments and demonstrating that there is no unique, complete proteome for the nucleolus, but rather an overlapping set of proteomes that are relevant to different cell states or conditions. ... [Information of the supplier]
The Barcoding Fauna Bavarica project is an All Species DNA barcoding campaign of the Zoologische Staatssammlung in Munich (ZSM) and the Canadian Centre for DNA Barcoding (CCDB). It represents a major component of Germany's contribution to the International Barcode of Life Project. Core funding comes from the Bavarian State Ministry of Science, Research, and the Arts, and from Genome Canada through the Ontario Genomics Institute. (Stefan Schmidt, unter https://www.youtube.com/watch?v=KOQEYZRrB-s). ... [Miscellaneous as indicated]