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Protocols

UCSC Xena specifications

Information


Unique identifier OMICS_17671
Name UCSC Xena
Alternative name UCSC Xena Browser
Interface Web user interface
Restrictions to use None
Programming languages Javascript, Shell (Bash), Other
License Apache License version 2.0
Computer skills Basic
Version 0.21.0
Stability Stable
Maintained Yes

Download


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Documentation


Maintainer


  • person_outline UCSC Xena Team

Information


Unique identifier OMICS_17671
Name UCSC Xena
Alternative name UCSC Xena Browser
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline UCSC Xena Team

Publication for UCSC Xena

UCSC Xena citations

 (36)
library_books

Preserved SCN4B expression is an independent indicator of favorable recurrence free survival in classical papillary thyroid cancer

2018
PLoS One
PMCID: 5933725
PMID: 29723302
DOI: 10.1371/journal.pone.0197007

[…] ologic diagnosis, histological types, gender, pathological stage, lymph nodal invasion, residual tumors, the history of radiation therapy, recurrence status and RFS in days were obtained by using the UCSC Xena Browser (https://xenabrowser.net/). In this patient cohort, the tumor tissue from 505 PTC cases (358 classical/usual cases, 102 follicular cases, 36 tall cell cases and 4 cases not specified […]

library_books

An integrated view of the role of miR 130b/301b miRNA cluster in prostate cancer

2018
PMCID: 5930504
PMID: 29744254
DOI: 10.1186/s40164-018-0102-0

[…] The datasets analyzed during the current study are available in the GEO and the UCSC Xena Browser.The datasets Martens-Uzunova et al. RNA-seq data [] was provided by the authors.Studies indicated as “NA” in column one of Table  were analyzed using data published within the origin […]

library_books

The Correlation Between the Immune and Epithelial Mesenchymal Transition Signatures Suggests Potential Therapeutic Targets and Prognosis Prediction Approaches in Kidney Cancer

2018
Sci Rep
PMCID: 5919934
PMID: 29700419
DOI: 10.1038/s41598-018-25002-w

[…] We used renal clear cell carcinoma (KIRC) data from the TCGA Data Portal (https://gdc-portal.nci.nih.gov/) and UCSC Xena project (http://xena.ucsc.edu), including RNAseqV2 and clinical data (n = 537). This study meets the publication guidelines provided by TCGA (http://cancergenome.nih.gov/publications/publica […]

library_books

SRARP and HSPB7 are epigenetically regulated gene pairs that function as tumor suppressors and predict clinical outcome in malignancies

2018
Mol Oncol
PMCID: 5928383
PMID: 29577611
DOI: 10.1002/1878-0261.12195

[…] The Cancer Genome Atlas Pan‐Cancer datasets were analyzed to examine the association of SRARP and HSPB7 methylation, expression, and mutations with survival. TCGA datasets were accessed using the UCSC Xena browser and bioinformatics tool (https://xenabrowser.net/). Duplicate samples were removed from the datasets before conducting survival analysis for primary tumors. In addition, TCGA data fr […]

library_books

Marker of proliferation Ki 67 expression is associated with transforming growth factor beta 1 and can predict the prognosis of patients with hepatic B virus related hepatocellular carcinoma

2018
PMCID: 5901156
PMID: 29692627
DOI: 10.2147/CMAR.S162595

[…] lyzed the gene patterns in chromosomes. The gene positions are based on GRCh38.p2 (NCBI). To detect the TGFB1 and MKI67 expression in different stages and types of liver cancer, we used GEPIA and the UCSC Xena project, which has recomputed all raw expression data from TCGA. Survival analysis was performed to evaluate the prognostic value of TGFB1 and MKI67 expression in liver cancer patients via G […]

call_split

SYK expression level distinguishes control from BRCA1 mutated lymphocytes

2018
PMCID: 5875411
PMID: 29618939
DOI: 10.2147/CMAR.S156359
call_split See protocol

[…] of BRCA1, BRCA2, and SYK genes across the breast tissues taken from healthy donors and patients with breast cancer (available from the GTEx and ICGC databases, respectively) were visualized using the UCSC Xena genome browser. In each database, samples were divided into two groups based on the expression of BRCA1 or BRCA2 genes using the median value as the cutoff point. The chart view option in Xe […]


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UCSC Xena institution(s)
UCSC Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA; BITS Pilani KK Birla Goa Campus, Goa, India
UCSC Xena funding source(s)
Supported by National Cancer Institute of the National Institutes of Health under award numbers 5U24CA180951-04 and 5U24CA210974-02.

UCSC Xena review

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Martin Abba

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Web
Beautiful app for data retrieval an visualization of different cancer genomics projects such as TCGA, ICGC, TARGET, etc. Also provide a set of analytic tools for survival analysis of selected features, correlation analysis, visualization of isoforms expression and mutation data.