The UCSC Table Browser data retrieval tool

Karolchik, Donna; Hinrichs, Angie S.; Furey, Terrence S.; Roskin, Krishna M.; Sugnet, Charles W.; Haussler, David; Kent, W. James

doi:10.1093/nar/gkh103

Cited by 2,092 publications

(1,949 citation statements)

References 10 publications

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“…Copy number variants overlapping centromeres or telomeres (as defined by UCSC (http://genome.ucsc.edu/) using the Table Browser Software (Karolchik et al ., 2004) and the GRCh37/hg19 genome build) were excluded, as were CNVs with a frequency < 1%.…”

Section: Methodsmentioning

confidence: 99%

Copy number variation associates with mortality in long‐lived individuals: a genome‐wide assessment

et al. 2015

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SummaryCopy number variants (CNVs) represent a significant source of genetic variation in the human genome and have been implicated in numerous diseases and complex traits. To date, only a few studies have investigated the role of CNVs in human lifespan. To investigate the impact of CNVs on prospective mortality at the extreme end of life, where the genetic component of lifespan appears most profound, we analyzed genomewide CNV data in 603 Danish nonagenarians and centenarians (mean age 96.9 years, range 90.0–102.5 years). Replication was performed in 500 long‐lived individuals from the Leiden Longevity Study (mean age 93.2 years, range 88.9–103.4 years). First, we assessed the association between the CNV burden of each individual (the number of CNVs, the average CNV length, and the total CNV length) and mortality and found a significant increase in mortality per 10 kb increase in the average CNV length, both for all CNVs (hazard ratio (HR) = 1.024, P = 0.002) and for duplications (HR = 1.011, P = 0.005), as well as per 100 kb increase in the total length of deletions (HR = 1.009, P = 0.0005). Next, we assessed the relation between specific deletions and duplications and mortality. Although no genome–wide significant associations were discovered, we identified six deletions and one duplication that showed consistent association with mortality in both or either of the sexes across both study populations. These results indicate that the genome–wide CNV burden, specifically the average CNV length and the total CNV length, associates with higher mortality in long‐lived individuals.

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Section: Methodsmentioning

confidence: 99%

Copy number variation associates with mortality in long‐lived individuals: a genome‐wide assessment

et al. 2015

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“…We used the NCBI protein tables for the ORF sequences. Since the Hi-C contact maps for mammals were based on the mm9/ hg18 versions of the genomes, we used the UCSC table browser tool 53 to generate3D genomic distance. We utilized the Hi-C contact maps to construct graph/ network representations of the spatial organization of the genome.…”

Section: Methodsmentioning

confidence: 99%

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

2014

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It has been shown that the distribution of genes in eukaryotic genomes is not random; however, formerly reported relations between gene function and genomic organization were relatively weak. Previous studies have demonstrated that codon usage bias is related to all stages of gene expression and to protein function. Here we apply a novel tool for assessing functional relatedness, codon usage frequency similarity (CUFS), which measures similarity between genes in terms of codon and amino acid usage. By analyzing chromosome conformation capture data, describing the three-dimensional (3D) conformation of the DNA, we show that the functional similarity between genes captured by CUFS is directly and very strongly correlated with their 3D distance in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, mouse and human. This emphasizes the importance of threedimensional genomic localization in eukaryotes and indicates that codon usage is tightly linked to genome architecture.

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“…Each CNV was validated on the reference sample, one fish presenting the same copy number status as the reference and two fish exhibiting copy number variability. Primers were designed using Primer3 (38) to amplify a 100-to 200-bp fragment within each CNV using sequences from the University of California Santa Cruz (UCSC) Genome Browser (39). A total of 100 CNV regions were randomly chosen for validation (Table S1).…”

Section: Methodsmentioning

confidence: 99%

“…Briefly, locations of the 6,080 CNVEs were assigned to the midpoint of a randomly selected probe on the Agilent array, and direct overlap with a zebrafish RefSeq gene was evaluated for 10,000 randomizations of CNVE sizes found in our analysis (SI Text). For enrichment analysis, RefSeq gene and assembly gap locations were extracted from the zebrafish reference genome using the "Table" function of the UCSC Genome Browser (39).…”

Section: Methodsmentioning

confidence: 99%

Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis

Brown

Dobrinski

Lee

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates and have been associated with numerous human diseases. Despite this, the extent of CNVs in the zebrafish, an important model for human disease, remains unknown. Using 80 zebrafish genomes, representing three commonly used laboratory strains and one native population, we constructed a genome-wide, high-resolution CNV map for the zebrafish comprising 6,080 CNV elements and encompassing 14.6% of the zebrafish reference genome. This amount of copy number variation is four times that previously observed in other vertebrates, including humans. Moreover, 69% of the CNV elements exhibited strain specificity, with the highest number observed for Tubingen. This variation likely arose, in part, from Tubingen's large founding size and composite population origin. Additional population genetic studies also provided important insight into the origins and substructure of these commonly used laboratory strains. This extensive variation among and within zebrafish strains may have functional effects that impact phenotype and, if not properly addressed, such extensive levels of germ-line variation and population substructure in this commonly used model organism can potentially confound studies intended for translation to human diseases.

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The UCSC Table Browser data retrieval tool

Cited by 2,092 publications

References 10 publications

Copy number variation associates with mortality in long‐lived individuals: a genome‐wide assessment

Copy number variation associates with mortality in long‐lived individuals: a genome‐wide assessment

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis

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