UCSC Cancer Genomics Browser protocols

UCSC Cancer Genomics Browser statistics

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UCSC Cancer Genomics Browser specifications

Information


Unique identifier OMICS_00925
Name UCSC Cancer Genomics Browser
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not maintained anymore.

Additional information


https://genome-cancer.ucsc.edu/proj/site/help/

Publications for UCSC Cancer Genomics Browser

UCSC Cancer Genomics Browser in pipelines

 (8)
2017
PMCID: 5470997
PMID: 28423715
DOI: 10.18632/oncotarget.16120

[…] sequence motifs for tfs. the gtex data were used to identify correlations between snps and whole blood-specific gene expression levels. the publically available cbioportal for cancer genomics [] and ucsc cancer genomics browser [] for oscc were utilized to analyse hmgb1 gene expression, enhancer modulation, molecular features, and clinical outcomes., we predicted targets using the web-based […]

2017
PMCID: 5709060
PMID: 29125844
DOI: 10.1371/journal.pcbi.1005840

[…] probes was analyzed for each cancer type., finally, tcga level-3 gene expression data measured by log transformed (base 2) rsem-normalized rna-seq (illumina hiseq) counts were downloaded from the ucsc cancer genomics browser (https://genome-cancer.ucsc.edu) on november 4, 2015., we defined driver genes as those reported by mutsigcv2 [] for each of the 18 cancer types; these data […]

2017
PMCID: 5739102
PMID: 28678605
DOI: 10.1080/15592294.2017.1342912

[…] environment. gene expression profiles of colon adenocarcinoma primary tumors (n = 241) and normal tissues (n = 39) measured by tcga using illumina hiseq 2000 rna-seq platform were downloaded via the ucsc cancer genomics browser website (level 3 rna-seq profiles, rnaseqv2 normalized rsem, feb 24, 2015 version). the differentially expressed gene list was produced using the r/bioconductor limma […]

2016
PMCID: 4729770
PMID: 26877780
DOI: 10.7150/thno.13178

[…] volumes were calculated using the following formula: tumor volume = length×width2×0.5., genomic analysis of brd4 was performed with tcga copy number portal (http://www.broadinstitute.org/tcga), ucsc cancer genomics browser , cbioportal for cancer genomics , and project achilles . gene set enrichment analysis was performed using the gsea software and microarray profiles were tested […]

2016
PMCID: 4879545
PMID: 27221742
DOI: 10.1038/srep26605

[…] motifs for tfs. the gtex data were used to identify the correlations between snps and whole-blood-specific gene expression levels. the publically available cbioportal for cancer genomics and ucsc cancer genomics browser for hepatocellular adenocarcinomas were utilized to analyse serpinb5 gene expression, dna methylation, molecular features, and clinical outcomes, a multiple sequence […]


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UCSC Cancer Genomics Browser in publications

 (75)
PMCID: 5898069
PMID: 29650031
DOI: 10.1186/s12967-018-1466-y

[…] and wrote the first draft. aslc, jy, kft and wk revised manuscript. all authors read and approved the final manuscript., we acknowledge the tcga research network (http://cancergenome.nih.gov/), the ucsc cancer genomics browser (https://genome-cancer.ucsc.edu/), and nci center for cancer genomics office (http://gdc.nci.nih.gov/) for providing the gastric cancer data set and analysis. we thank […]

PMCID: 5848567
PMID: 29530061
DOI: 10.1186/s13046-018-0711-9

[…] protocol was approved by and in accordance with the guidance of the research ethics committee of shanghai jiao tong university of medicine, shanghai, china. the cancer browser was linked from the ucsc cancer genomics browser (https://genome-cancer.ucsc.edu/), colorectal cancer was chosen and then downloaded related datasets. scd1 items were searched and summed up and then we combined scd1 […]

PMCID: 5785960
PMID: 29374236
DOI: 10.1038/s41598-018-20086-w

[…] cohorts. all clinical and gene expression data were collected previously and are available in public databases. gene expression and somatic mutation data from tcga (n = 513) were downloaded from the ucsc cancer genomics browser (https://genome-cancer.ucsc.edu/). data from the institute for medical informatics, statistics, and epidemiology (leipzig cohort [gse65858], n = 270) and the fhcrc […]

PMCID: 5833783
PMID: 29367737
DOI: 10.1038/s41419-017-0134-0

[…] information , the online version of this article 10.1038/s41419-017-0134-0 contains supplementary material., we acknowledge the tcga research network (http://cancergenome.nih.gov/), the ucsc cancer genomics browser (https://genome-cancer.ucsc.edu/), and nci center for cancer genomics office (http://gdc.nci.nih.gov/) for providing the gastric cancer data set and analysis. this study […]

PMCID: 5871081
PMID: 29599910
DOI: 10.18632/oncotarget.23663

[…] of cancer types [, ]. assembling this mean-normalized rna sequencing data provides the opportunity to evaluate genes of interest across a spectrum of cancer cohorts and is possible using the ucsc cancer genomics browser (https://genome-cancer-ucsc.edu) []. again, genes pertaining to our resistant signature appear much more likely to be detected within the 266 curated serous ovarian tcga […]


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UCSC Cancer Genomics Browser institution(s)
Department of Biomolecular Engineering, Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA, USA

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