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UCSC Genome Browser specifications


Unique identifier OMICS_29840
Name UCSC Genome Browser
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • person_outline bigWig format Team
  • person_outline Matthew Speir

Additional information


Publications for UCSC Genome Browser


The UCSC Genome Browser.

2012 Curr Protoc Bioinformatics
PMID: 23255150
DOI: 10.1002/0471250953.bi0104s40

The UCSC Genome Browser.

2011 Curr Protoc Hum Genet
PMCID: 3222792
PMID: 21975940
DOI: 10.1002/0471142905.hg1806s71

The UCSC Genome Browser.

2009 Curr Protoc Bioinformatics
PMCID: 2834533
PMID: 19957273
DOI: 10.1002/0471250953.bi0104s28

The UCSC Genome Browser.

2007 Curr Protoc Bioinformatics
PMID: 18428780
DOI: 10.1002/0471250953.bi0104s17

UCSC Genome Browser citations


Novel internal regulators and candidate miRNAs within miR 379/miR 656 miRNA cluster can alter cellular phenotype of human glioblastoma

Sci Rep
PMCID: 5955984
PMID: 29769662
DOI: 10.1038/s41598-018-26000-8

[…] The genomic sequence of C14-IP-3 was obtained from UCSC Genome Browser, and was subjected through sgRNA predicting software of CRISPRSCAN, with information on human genome off-targets. A total of 10 sgRNAs could be designed against C14-IP-3. We have u […]


Direct measurement of pervasive weak repression by microRNAs and their role at the network level

BMC Genomics
PMCID: 5952853
PMID: 29764374
DOI: 10.1186/s12864-018-4757-z

[…] targeted by miR310s were identified using the TargetScan algorithm [, , , ]. 3’UTR annotation was extracted from BDGP6.83. The whole genome alignments were dm6, droSim1, and droYak3 available at the UCSC Genome Browser. miRNA expression during the L3 larval stage was ranked according to previous studies [, ]. […]


CD82 hypomethylation is essential for tuberculosis pathogenesis via regulation of RUNX1 Rab5/22

PMCID: 5951854
PMID: 29760437
DOI: 10.1038/s12276-018-0091-4
call_split See protocol

[…] ed as showing a 1.0 log2-fold difference and P-adj < 0.01 in expression between MTB Rv and MTB Ra. RNA-seq experiments were normalized and visualized using HOMER after preparing custom tracks for the UCSC Genome Browser (http://genome.ucsc.edu/). […]


The lncRNA myocardial infarction associated transcript centric competing endogenous RNA network in non small cell lung cancer

PMCID: 5958945
DOI: 10.2147/CMAR.S163395

[…] ga/). Both RNA-seq data and miRNA-seq data of tumor tissues and adjacent non-tumor tissues were included, according to the histologic staging data. lncRNA and mRNA transcripts were annotated based on UCSC Genome Browser database (http://www.genome.ucsc.edu) database. After nor-malization of expression data, the DESeq package in R was used to identify the DEGs. Absolute fold change (including upreg […]


Recently evolved human specific methylated regions are enriched in schizophrenia signals

BMC Evol Biol
PMCID: 5946405
PMID: 29747567
DOI: 10.1186/s12862-018-1177-2

[…] ccelerated in primates; and pHARs, in which regions conserved in primates (but not other mammals) are accelerated in humans. Conversion to hg19 assembly was performed using the liftOver tool from the UCSC Genome Browser. […]


TGF β induces miR 100 and miR 125b but blocks let 7a through LIN28B controlling PDAC progression

Nat Commun
PMCID: 5945639
PMID: 29748571
DOI: 10.1038/s41467-018-03962-x

[…] babraham.ac.uk/projects/fastqc/). The reads from the fastq files, for each sample, were then mapped on the reference human genome, version hg19, obtained from the University of California Santa Cruz (UCSC) genome browser (https://genome.ucsc.edu/) by using TopHat. For isoform level analysis (miRNA target identification) RPKM normalized values were produced with Partek Genomic Suit software (Partek […]

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UCSC Genome Browser institution(s)
Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA; Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
UCSC Genome Browser funding source(s)
Supported by National Human Genome Research Institute [4U41HG002371; 5U41HG007234; 5U54HG007990]; NIH [1U01MH114825]; California Institute for Regenerative Medicine [GC1R-06673-C]; Howard Hughes Medical Institute [090100]; Regeneron [CBJCHBCAABAAnBGXMxFrE0WG7VvHOtm8RAzv674WMNt]; St. Baldricks Foundation [427053]; Silicon Valley Community Foundation [2018-182809; 2017-171519].

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