Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.
paper
Cited
Public
- Authors
- Raney, Brian J; Dreszer, Timothy R; Barber, Galt P; Clawson, Hiram; Fujita, Pauline A; Wang, Ting; Nguyen, Ngan; Paten, Benedict; Zweig, Ann S; Karolchik, Donna; Kent, W James
- Year
- 2014
- Journal
- Bioinformatics (Oxford, England)
- PMID
- 24227676
- DOI
- 10.1093/bioinformatics/btt637
- PMCID
- PMC3967101
SUMMARY: Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations. Hub datasets can be organized, configured and fully integrated into the University of California Santa Cruz (UCSC) Genome Browser and accessed through the familiar browser interface. For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror. AVAILABILITY AND IMPLEMENTATION: Source code for the BigWig, BigBed and Genome Browser software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/. Binary Alignment/Map (BAM) and Variant Call Format (VCF)/tabix utilities are available from http://samtools.sourceforge.net/ and http://vcftools.sourceforge.net/. The UCSC Genome Browser is publicly accessible at http://genome.ucsc.edu.
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| Name | Type |
|---|---|
| copy number variant | variant |
| insertion/deletion | variant |
| single nucleotide variant | variant |
| structural variant | cohort |
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In this knowledge base
| Title | Year | PMID |
|---|---|---|
| A protocadherin gene cluster regulatory variant is associated with nicotine withdrawal and the urge to smoke. | 2017 | 27067016 |
| The UCSC Genome Browser database: 2014 update. | 2014 | 24270787 |
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| Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2. | Shen F et al. | — | 2020 | → |
| ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments. | Chèneby J et al. | — | 2020 | → |
| Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina. | Chang E et al. | — | 2020 | → |
| The African Swine Fever Virus Transcriptome. | Cackett G et al. | — | 2020 | → |
| The Paralogous Krüppel-like Factors 9 and 13 Regulate the Mammalian Cellular Circadian Clock Output Gene <i>Dbp</i>. | Knoedler JR et al. | — | 2020 | → |
| The UCSC SARS-CoV-2 Genome Browser. | Fernandes JD et al. | — | 2020 | → |
| Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns. | Farmiloe G et al. | — | 2020 | → |
| A gene expression atlas of embryonic neurogenesis in <i>Drosophila</i> reveals complex spatiotemporal regulation of lncRNAs. | McCorkindale AL et al. | — | 2019 | → |
| A Heterochromatin-Specific RNA Export Pathway Facilitates piRNA Production. | ElMaghraby MF et al. | — | 2019 | → |
| A practical guide for DNase-seq data analysis: from data management to common applications. | Liu Y et al. | — | 2019 | → |
| BarkBase: Epigenomic Annotation of Canine Genomes. | Megquier K et al. | — | 2019 | → |
| BCAT1 and miR-2504: novel methylome signature distinguishes spindle/desmoplastic melanoma from superficial malignant peripheral nerve sheath tumor. | Jour G et al. | — | 2019 | → |
| Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. | Zheng R et al. | — | 2019 | → |
| Clinical Implications of Sub-grouping HER2 Positive Tumors by Amplicon Structure and Co-amplified Genes. | Maoz M et al. | — | 2019 | → |
| CORR® ORS Richard A. Brand Award: Disruption in Peroxisome Proliferator-Activated Receptor-γ (PPARG) Increases Osteonecrosis Risk Through Genetic Variance and Pharmacologic Modulation. | Wyles CC et al. | — | 2019 | → |
| Database resources of the National Center for Biotechnology Information. | Sayers EW et al. | — | 2019 | → |
| Ensembl 2019. | Cunningham F et al. | — | 2019 | → |
| Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. | Farré M et al. | — | 2019 | → |
| Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy. | Arbel H et al. | — | 2019 | → |
| Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap. | Giuffra E et al. | — | 2019 | → |
| Functional characterization of <i>CNOT3</i> variants identified in familial adenomatous polyposis adenomas. | Delacruz RGC et al. | — | 2019 | → |
| Genetic Variations and Precision Medicine. | Alzu'bi AA et al. | — | 2019 | → |
| Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. | Kolchanova S et al. | — | 2019 | → |
| G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes. | Liu Y et al. | — | 2019 | → |
| HTLV-1 basic leucine zipper factor protects cells from oxidative stress by upregulating expression of Heme Oxygenase I. | Rushing AW et al. | — | 2019 | → |
| LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data. | Jiang L et al. | — | 2019 | → |
| LNCipedia 5: towards a reference set of human long non-coding RNAs. | Volders PJ et al. | — | 2019 | → |
| MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs. | Hoff KJ | — | 2019 | → |
| Novel Neonatal Variants of the Carbamoyl Phosphate Synthetase 1 Deficiency: Two Case Reports and Review of Literature. | Yan B et al. | — | 2019 | → |
| Nucleotide Resolution Comparison of Transcription of Human Cytomegalovirus and Host Genomes Reveals Universal Use of RNA Polymerase II Elongation Control Driven by Dissimilar Core Promoter Elements. | Parida M et al. | — | 2019 | → |
| PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP. | Ramani R et al. | — | 2019 | → |
| Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues. | Moon JM et al. | — | 2019 | → |
| The Rich World of p53 DNA Binding Targets: The Role of DNA Structure. | Brázda V et al. | — | 2019 | → |
| The UCSC Genome Browser database: 2019 update. | Haeussler M et al. | — | 2019 | → |
| TogoGenome/TogoStanza: modularized Semantic Web genome database. | Katayama T et al. | — | 2019 | → |
| UniProt genomic mapping for deciphering functional effects of missense variants. | McGarvey PB et al. | — | 2019 | → |
| Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. | Lizio M et al. | — | 2019 | → |
| A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women. | Bensen JT et al. | — | 2018 | → |
| BRD4 regulates cellular senescence in gastric cancer cells via E2F/miR-106b/p21 axis. | Dong X et al. | — | 2018 | → |
| ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. | Oki S et al. | — | 2018 | → |
| Comparative Genome Annotation. | König S et al. | — | 2018 | → |
| Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA). | Richard Albert J et al. | — | 2018 | → |
| Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. | Kersey PJ et al. | — | 2018 | → |
| Epigenetic and transcriptional dysregulation of VWA2 associated with a MYC-driven oncogenic program in colorectal cancer. | González B et al. | — | 2018 | → |
| Evolutionary expansion of DNA hypomethylation in the mammalian germline genome. | Qu J et al. | — | 2018 | → |
| FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment. | Dimitrova E et al. | — | 2018 | → |
| Genome-wide association study (GWAS) of ovarian cancer in Japanese predicted regulatory variants in 22q13.1. | Yodsurang V et al. | — | 2018 | → |
| JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. | Khan A et al. | — | 2018 | → |
| Maternal 5<sup>m</sup>CpG Imprints at the <i>PARD6G-AS1</i> and <i>GCSAML</i> Differentially Methylated Regions Are Decoupled From Parent-of-Origin Expression Effects in Multiple Human Tissues. | de Sá Machado Araújo G et al. | — | 2018 | → |
| miR-181a regulates erythroid enucleation <i>via</i> the regulation of Xpo7 expression. | Figueroa AA et al. | — | 2018 | → |
| miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential. | Meyer SE et al. | — | 2018 | → |
| Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database. | James-Zorn C et al. | — | 2018 | → |
| ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. | Chèneby J et al. | — | 2018 | → |
| Revealing a human p53 universe. | Nguyen TT et al. | — | 2018 | → |
| The Encyclopedia of DNA elements (ENCODE): data portal update. | Davis CA et al. | — | 2018 | → |
| The UCSC Genome Browser database: 2018 update. | Casper J et al. | — | 2018 | → |
| Updates on resources, software tools, and databases for plant proteomics in 2016-2017. | Misra BB | — | 2018 | → |
| Using WormBase ParaSite: An Integrated Platform for Exploring Helminth Genomic Data. | Bolt BJ et al. | — | 2018 | → |
| Whole Genome Sequencing, <i>de Novo</i> Assembly and Phenotypic Profiling for the New Budding Yeast Species <i>Saccharomyces jurei</i>. | Naseeb S et al. | — | 2018 | → |
| X-Chromosome Inactivation and Escape from X Inactivation in Mouse. | Ma W et al. | — | 2018 | → |
| A case of Feingold type 2 syndrome associated with keratoconus refines keratoconus type 7 locus on chromosome 13q. | Sirchia F et al. | — | 2017 | → |
| A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data. | Li S et al. | — | 2017 | → |
| A Golden Age for Working with Public Proteomics Data. | Martens L et al. | — | 2017 | → |
| A heterochromatin-dependent transcription machinery drives piRNA expression. | Andersen PR et al. | — | 2017 | → |
| A protocadherin gene cluster regulatory variant is associated with nicotine withdrawal and the urge to smoke. | Jensen KP et al. | — | 2017 | → |
| Big Data access and infrastructure for modern biology: case studies in data repository utility. | Boles NC et al. | — | 2017 | → |
| C1orf64 is a novel androgen receptor target gene and coregulator that interacts with 14-3-3 protein in breast cancer. | Naderi A | — | 2017 | → |
| Clinical Features, Molecular Heterogeneity, and Prognostic Implications in YARS2-Related Mitochondrial Myopathy. | Sommerville EW et al. | — | 2017 | → |
| DNA Methylation-Based Classifier for Accurate Molecular Diagnosis of Bone Sarcomas. | Wu SP et al. | — | 2017 | → |
| Ensembl 2017. | Aken BL et al. | — | 2017 | → |
| Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona. | Gandhi S et al. | — | 2017 | → |
| Exome Sequencing of Extended Families with Alzheimer's Disease Identifies Novel Genes Implicated in Cell Immunity and Neuronal Function. | Cukier HN et al. | — | 2017 | → |
| Exome sequencing reveals novel IRXI mutation in congenital heart disease. | Guo C et al. | — | 2017 | → |
| FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies. | Abugessaisa I et al. | — | 2017 | → |
| FANTOM5 CAGE profiles of human and mouse samples. | Noguchi S et al. | — | 2017 | → |
| Genome Annotation. | Abugessaisa I et al. | — | 2017 | → |
| Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos. | Hodonsky CJ et al. | — | 2017 | → |
| Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions. | Guo C et al. | — | 2017 | → |
| Genome-wide prediction of DNase I hypersensitivity using gene expression. | Zhou W et al. | — | 2017 | → |
| Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation. | Sharma V et al. | — | 2017 | → |
| INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions. | Berry CC et al. | — | 2017 | → |
| Loss of β-catenin in resident cardiac fibroblasts attenuates fibrosis induced by pressure overload in mice. | Xiang FL et al. | — | 2017 | → |
| Low-cell-number, single-tube amplification (STA) of total RNA revealed transcriptome changes from pluripotency to endothelium. | Lee YH et al. | — | 2017 | → |
| miRNA-122 Protects Mice and Human Hepatocytes from Acetaminophen Toxicity by Regulating Cytochrome P450 Family 1 Subfamily A Member 2 and Family 2 Subfamily E Member 1 Expression. | Chowdhary V et al. | — | 2017 | → |
| NGSmethDB 2017: enhanced methylomes and differential methylation. | Lebrón R et al. | — | 2017 | → |
| Sex chromosomes drive gene expression and regulatory dimorphisms in mouse embryonic stem cells. | Werner RJ et al. | — | 2017 | → |
| Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. | Serres-Armero A et al. | — | 2017 | → |
| SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. | Hitz BC et al. | — | 2017 | → |
| The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. | Dreos R et al. | — | 2017 | → |
| The human-induced pluripotent stem cell initiative-data resources for cellular genetics. | Streeter I et al. | — | 2017 | → |
| The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data. | Clarke L et al. | — | 2017 | → |
| The UCSC Genome Browser database: 2017 update. | Tyner C et al. | — | 2017 | → |
| Tissue resolved, gene structure refined equine transcriptome. | Mansour TA et al. | — | 2017 | → |
| Transcription Factor CTIP1/ BCL11A Regulates Epidermal Differentiation and Lipid Metabolism During Skin Development. | Li S et al. | — | 2017 | → |
| Transethnic insight into the genetics of glycaemic traits: fine-mapping results from the Population Architecture using Genomics and Epidemiology (PAGE) consortium. | Bien SA et al. | — | 2017 | → |
| Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. | Lizio M et al. | — | 2017 | → |
| WormBase ParaSite - a comprehensive resource for helminth genomics. | Howe KL et al. | — | 2017 | → |
| A scientist's guide for submitting data to ZFIN. | Howe DG et al. | — | 2016 | → |
| A systematic, large-scale comparison of transcription factor binding site models. | Hombach D et al. | — | 2016 | → |
| Cistrome-based Cooperation between Airway Epithelial Glucocorticoid Receptor and NF-κB Orchestrates Anti-inflammatory Effects. | Kadiyala V et al. | — | 2016 | → |
| Defining the identity of mouse embryonic dermal fibroblasts. | Budnick I et al. | — | 2016 | → |
| ENCODE data at the ENCODE portal. | Sloan CA et al. | — | 2016 | → |
| Ensembl 2016. | Yates A et al. | — | 2016 | → |
| Ensembl Genomes 2016: more genomes, more complexity. | Kersey PJ et al. | — | 2016 | → |
| Flexible Data Analysis Pipeline for High-Confidence Proteogenomics. | Weisser H et al. | — | 2016 | → |
| Genotoxicity in Mice Following AAV Gene Delivery: A Safety Concern for Human Gene Therapy? | Chandler RJ et al. | — | 2016 | → |
| <i>SORL1</i> mutations in early- and late-onset Alzheimer disease. | Cuccaro ML et al. | — | 2016 | → |
| PGD: a pangolin genome hub for the research community. | Tan TK et al. | — | 2016 | → |
| Semi-automated genome annotation using epigenomic data and Segway | Roberts EG et al. | — | 2016 | — |
| The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors. | Wiechens N et al. | — | 2016 | → |
| The International Human Epigenome Consortium Data Portal. | Bujold D et al. | — | 2016 | → |
| The UCSC Genome Browser database: 2016 update. | Speir ML et al. | — | 2016 | → |
| Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners. | Alves da Silva AF et al. | — | 2016 | → |
| UCSC Data Integrator and Variant Annotation Integrator. | Hinrichs AS et al. | — | 2016 | → |
| A New Noncoding RNA Arranges Bacterial Chromosome Organization. | Qian Z et al. | — | 2015 | → |
| An interactive genome browser of association results from the UK10K cohorts project. | Geihs M et al. | — | 2015 | → |
| ChromContact: A web tool for analyzing spatial contact of chromosomes from Hi-C data. | Sato T et al. | — | 2015 | → |
| Compound heterozygous NOTCH1 mutations underlie impaired cardiogenesis in a patient with hypoplastic left heart syndrome. | Theis JL et al. | — | 2015 | → |
| Current methods for automated annotation of protein-coding genes. | Hoff KJ et al. | — | 2015 | → |
| Dataset of transcriptional landscape of B cell early activation. | Garruss AS et al. | — | 2015 | → |
| Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. | Verfaillie A et al. | — | 2015 | → |
| DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. | Molyneaux BJ et al. | — | 2015 | → |
| Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. | Jaffe AE et al. | — | 2015 | → |
| Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data. | Haase K et al. | — | 2015 | → |
| Divergence of transcriptional landscape occurs early in B cell activation. | Fowler T et al. | — | 2015 | → |
| DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. | Blin K et al. | — | 2015 | → |
| Extending reference assembly models. | Church DM et al. | — | 2015 | → |
| Genome-wide variant analysis of simplex autism families with an integrative clinical-bioinformatics pipeline. | Jiménez-Barrón LT et al. | — | 2015 | → |
| Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations. | Pybus M et al. | — | 2015 | → |
| Identification of copy number variations in Qinchuan cattle using BovineHD Genotyping Beadchip array. | Zhang Q et al. | — | 2015 | → |
| Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. | Ernst J et al. | — | 2015 | → |
| Navigating protected genomics data with UCSC Genome Browser in a Box. | Haeussler M et al. | — | 2015 | → |
| Recessive MYH6 Mutations in Hypoplastic Left Heart With Reduced Ejection Fraction. | Theis JL et al. | — | 2015 | → |
| The Genome 10K Project: a way forward. | Koepfli KP et al. | — | 2015 | → |
| The UCSC Genome Browser database: 2015 update. | Rosenbloom KR et al. | — | 2015 | → |
| ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines. | Wolfinger MT et al. | — | 2015 | → |
| ChIPseek, a web-based analysis tool for ChIP data. | Chen TW et al. | — | 2014 | → |
| Comparative assembly hubs: web-accessible browsers for comparative genomics. | Nguyen N et al. | — | 2014 | → |
| The rhino-deadlock-cutoff complex licenses noncanonical transcription of dual-strand piRNA clusters in Drosophila. | Mohn F et al. | — | 2014 | → |
| The UCSC Ebola Genome Portal. | Haeussler M et al. | — | 2014 | → |
| The UCSC Genome Browser database: 2014 update. | Karolchik D et al. | — | 2014 | → |
| Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. | Green RE et al. | — | 2014 | → |
| Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment. | Han BY et al. | — | 2014 | → |