The UCSC Genome Browser database: 2014 update

By Donna Karolchik, Galt P. Barber, Jonathan Casper, Hiram Clawson, Melissa S. Cline, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadoo, Maximilian Haeussler and 15 more. Nucleic Acids Res., 2013

915 citations recorded by the source corpus.

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser’s web-based tools provide an integrated environment for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic data sets. As of September 2013, the database contained genomic sequence and a basic set of annotation ‘tracks’ for ∼90 organisms. Significant new annotations include a 60-species multiple alignment conservation track on the mouse, updated UCSC Genes tracks for human and mouse, and several new sets of variation and ENCODE data. New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants uploaded as a custom track, an extension to UCSC Genes that displays haplotype alleles for protein-coding genes and an expansion of data hubs that includes the capability to display remotely hosted user-provided assembly sequence in addition to annotation data. To improve European access, we have added a Genome Browser mirror (http://genome-euro.ucsc.edu) hosted at Bielefeld University in Germany.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/60add4035c2b6d4b9888cb1028c31e6bed793d60

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Citations in the corpus

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways (2015, background): “Three-dimensional objects are often used for representing protein structures [1, 2], one-dimensional tracks for genome sequences [3, 4], force-directed graphs for interaction networks [5], trees for phylogenetic relationships [6, 7].”
The UCSC Genome Browser database: 2015 update (2014, background): “The UCSC Genome Browser database (1,2) is a large collection of genome assemblies and annotations for vertebrate and selected model organisms that has been under active development since 2000.”
Selecting causal genes from genome-wide association studies via functionally-coherent subnetworks (2014, methodology): “Transcripts corresponding to these genes were mapped to UCSC hg19 coordinates 44 .”
DNA methylation aging clocks: challenges and recommendations (2019, background): “NC, not covered CpGs in this Combined Segmentation overlap; f Gencode [132] Exon and Transcripts; g UCSC [133]-defined CpG islands and shore regions (+/−2 kb); h Major repeat classes (UCSC RepeatMasker [133]), including DNA repeat elements (DNA_repeats), long”
The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools (2014, methodology): “sapiens CAGE from ENCODE/RIKEN, downloaded from UCSC genome browser database (12) 148 3841”
Genenames.org: the HGNC resources in 2015 (2014, background): “HGNC symbols and names are seen as a standard and used in all the major databases that concentrate on human genes and proteins, such as Ensembl (2), UniProt (3), NCBI Gene (4), ENA/GenBank/DDBJ (5–7), Vega (8), GeneCards (9) and the UCSC genome browser (10), as well as disease and phenotype resource”
tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes (2016, background): “Finally, links from either the GtRNAdb gene page, or the list of perfect matching hits shows the tRNA gene in the interactive UCSC Genome Browser with tracks that show the level of multi-genome conservation among six other yeast species, the positions of previously noted modifications, tRNA-seq expr”
Ensembl comparative genomics resources (2016, background): “Multiple alignments from UCSC are not synchronized across species however: the human GRCh37 assembly (hg19) genome browser includes a 100 species multiple alignment, which includes the mouse GRCm38 (mm10) assembly, but the corresponding mouse genome browser provides only a 60-way multiple alignment ”
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads (2015, methodology): “We used Flux Simulator 23 to generate 150 million 75-bp paired-end reads, extracted from all RefSeq human transcripts as provided by the UCSC Genome Browser 24 .”
Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity (2015, neutral): “Genomic coordinates of variants from alignments to human reference assembly NCBI36 (hg18) were converted to GRCh37 using LiftOver 47 with an Ensembl chain file (see URLs).”
Ensembl comparative genomics resources (2016, background): “Multiple alignments from UCSC are not synchronized across species however: the human GRCh37 assembly (hg19) genome browser includes a 100 species multiple alignment, which includes the mouse GRCm38 (mm10) assembly, but the corresponding mouse genome browser provides only a 60-way multiple alignment ”