数据库的一些名词解释

Recombination rate (cM/Mb)Fine-scale recombination rates (cM/Mb) as estimated fromPhase II HapMap data (release 21) using the methods describedin McVean et al. (2004) and Winckler et al. (2005). See READMEin /downloads/recombination/latest/ for details.Genotyped SNPsSNPs in dbSNP genotyped by the HapMap Project. For regionswith very high SNP density, this track is turned off and a bardensity graph showing genotyped SNPs/20Kb is shown instead. dbSNP SNPsReference SNP clusters (rsEntrez genesmRNA sequences from NCBI's RefSeq resource. Annotationsfrom the UCSC Genome Browser Database (refGene.txt.gz,refLink.txt.gz, refSeqSummary.txt.gz). Both RefSeq shortdescriptions and longer summaries (for annotated genes) aresearchable, but only short descriptions are displayed alongsidefeatures.Ensembl genesmRNA sequences from Ensembl (NCBI Build 35).Sequence Tagged SitesSequence Tagged Sites from NCBI's UniSTSrepository.Annotations from the UCSC Genome BrowserDatabase (refGene.txt.gz).ContigsNT contigs created during the construction of the genomeassembly. Annotations from the UCSC Genome BrowserDatabase (ctgPos.txt.gz).3-frame translation (forward)This track shows the position of stop codons at lowmagnifications, and the 3-frame translation at highmagnifications. Only the forward strand is shown.DNA/GC Content沒有額外的相關信息.3-frame translation (reverse)This track shows the position of stop codons at lowmagnifications, and the 3-frame translation at highmagnifications. Only the reverse strand is shown.Reactome pathwaysGenes with pathway annotations inthe Reactome knowledgebase (Reactome version 33). Genomic Variants (Redon et al.)Copy number polymorphisms identified in HapMap samples viathe 500K EA and WGTP array platforms (Redon et al. 2007).Color code: green indicates a genomic gain (insertion); redindicates a loss (deletion); pink indicates both, a gain and a loss(insertion and deletion); blue indicates an inversion; blackindicates a variant of undefined type. Number in parenthesisindicates the number of samples bearing the variant. Source ofdata: Database of Genomic Variants.Genomic Variants (Iafrate et al.)Copy number polymorphisms from BAC microarray analysis(Iafrate et al. 2004). Color code: green indicates a genomic gain(insertion); red indicates a loss (deletion); pink indicates both, again and a loss (insertion and deletion); blue indicates aninversion; black indicates a variant of undefined type. Number inparenthesis indicates the number of samples bearing the variant.Source of data: Database of Genomic Variants.Genomic Variants (Tuzun et al.)Copy number polymorphisms (Tuzun et al. 2005). Color code:green indicates a genomic gain (insertion); red indicates a loss(deletion); pink indicates both, a gain and a loss (insertion anddeletion); blue indicates an inversion; black indicates a variant ofundefined type. Number in parenthesis indicates the number ofsamples bearing the variant. Source of data: Database ofGenomic Variants.Genomic Variants (Mills et al.)Copy number polymorphisms (Mills et al. 2006). Color code:green indicates a genomic gain (insertion); red indicates a loss(deletion); pink indicates both, a gain and a loss (insertion anddeletion); blue indicates an inversion; black indicates a variant ofundefined type. Number in parenthesis indicates the number ofsamples bearing the variant. Source of data: Database ofGenomic Variants.Genomic Variants (Simon-Sanchez et al.)Copy number polymorphisms (Simon-Sanchez et al. 2007).Color code: green indicates a genomic gain (insertion); redindicates a loss (deletion); pink indicates both, a gain and a loss(insertion and deletion); blue indicates an inversion; blackindicates a variant of undefined type. Number in parenthesisindicates the number of samples bearing the variant. Source ofdata: Database of Genomic Variants.Genomic Variants (Locke et al.)Copy number polymorphisms (Locke et al. 2006). Color code:green indicates a genomic gain (insertion); red indicates a loss(deletion); pink indicates both, a gain and a loss (insertion anddeletion); blue indicates an inversion; black indicates a variant ofundefined type. Number in parenthesis indicates the number ofsamples bearing the variant. Source of data: Database ofGenomic Variants.Genomic Variants (Sebat et al.)Copy number polymorphisms (Sebat et al. 2004). Color code:green indicates a genomic gain (insertion); red indicates a loss(deletion); pink indicates both, a gain and a loss (insertion anddeletion); blue indicates an inversion; black indicates a variant ofundefined type. Number in parenthesis indicates the number ofsamples bearing the variant. Source of data: Database ofGenomic Variants.Genomic Variants (Wong et al.)Copy number polymorphisms (Wong et al. 2007). Color code:green indicates a genomic gain (insertion); red indicates a loss(deletion); pink indicates both, a gain and a loss (insertion anddeletion); blue indicates an inversion; black indicates a variant ofundefined type. Number in parenthesis indicates the number ofsamples bearing the variant. Source of data: Database ofGenomic Variants.Genomic Variants (Sharp et al.)Copy number polymorphisms (Sharp et al. 2005). Color code:green indicates a genomic gain (insertion); red indicates a loss(deletion); pink indicates both, a gain and a loss (insertion anddeletion); blue indicates an inversion; black indicates a variant ofundefined type. Number in parenthesis indicates the number ofsamples bearing the variant. Source of data: Database ofGenomic Variants.Deletions (McCarroll et al.)Deletions from Analysis of HapMap genotyping data (McCarrollet al. 2006). Number in parenthesis indicates the number ofsamples bearing the variant. Source of data: Database ofGenomic Variants.Deletions (Conrad et al.)Deletions from Analysis of HapMap genotyping data (Conrad etal. 2005). Number in parenthesis indicates the number ofsamples bearing the variant. Source of data: Database ofGenomic Variants.Deletions (Hinds et al.)Deletions from from haploid hybridization analysis (Hinds et al.2005). Number in parenthesis indicates the number of samplesbearing the variant. Source of data: Database of GenomicVariants.Genome-Wide Association studies (NHGRI Catalog)Genetic variants reported to confer risk or susceptibility to a traitor disease. Data taken from the NHGRI's Catalog of PublishedGenome-Wide Association Studies. Visualize data inthe GWAs karyogram.OMIM disease associationsThe OMIM_asssociations track from the MutaGeneSysdatabase links SNP data from HapMap and Whole GenomeAssociation Studies (WGAS) to the known disease variantsreported by the Online Mendelian Inheritance in Man (OMIM).The track includes two classes of features mapped to theHapMap Genome Browser: 1). Direct association: the feature isa HapMap SNP that appears in OMIM, and 2). Indirectassociation: the feature is a SNP on a WGAS array thatparticipates in the best predictor of an OMIM disease variant.Please see the MutaGeneSys project page for a completedescription.。