PCAWG statistics

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Protocols

PCAWG specifications

Information


Unique identifier OMICS_21887
Name PCAWG
Alternative name PanCancer Analysis of Whole Genomes
Restrictions to use None
Community driven Yes
Data access File download, Browse, Application programming interface
User data submission Allowed
Version 1.0
Maintained Yes

Subtools


  • EBI Expression Atlas
  • IGCG Data Portal
  • PCAWG-Scout
  • UCSC Xena

Maintainers


  • person_outline Alvis Brazma
  • person_outline Gunnar Rätsch
  • person_outline Angela Brooks
  • person_outline Team PCAWG

Publications for PanCancer Analysis of Whole Genomes

PCAWG citations

 (41)
library_books

Histone H4 acetylation regulates behavioral inter individual variability in zebrafish

2018
Genome Biol
PMCID: 5922312
PMID: 29695303
DOI: 10.1186/s13059-018-1428-y

[…] ChIP-seq and RNA-seq data are stored in the ArrayExpress repository (E-MTAB-5993 and E-MTAB-5992, respectively) [, ]. RNA-seq data have also been included as part of the EBI expression atlas (http://www.ebi.ac.uk/gxa). The video trajectories of the fish experiments presented in the manuscript are available on Figshare []. The ad hoc MATLAB functions for obtaining the […]

call_split

Genome Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds

2018
Front Genet
PMCID: 5902979
PMID: 29692799
DOI: 10.3389/fgene.2018.00118
call_split See protocol

[…] ein interaction network for the candidate genes using the STRING database version 10.5 (). In addition, differential expressions of the candidate genes in various tissues were examined using the EMBL-EBI Expression Atlas database (). […]

call_split

Cardiac arrhythmia and neuroexcitability gene variants in resected brain tissue from patients with sudden unexpected death in epilepsy (SUDEP)

2018
PMCID: 5869741
PMID: 29619247
DOI: 10.1038/s41525-018-0048-5
call_split See protocol

[…] of identified variants that were unique to SUDEP was assessed. The analytical work flow is summarized in Fig. . Gene expression patterns in humans for select genes were assessed by querying the EMBL-EBI Expression Atlas. […]

library_books

Blockade of Tumor Expressed PD 1 promotes lung cancer growth

2018
PMCID: 5889288
PMID: 29632720
DOI: 10.1080/2162402X.2017.1408747

[…] To validate our findings of cancer-intrinsic PD-1 expression in human NSCLC, we queried the EMBL-EBI Expression Atlas for human NSCLC cell lines in culture rather than lung cancer tissues, which are likely to be infiltrated with PD-1-expressing lymphocytes. Four RNA-sequenced data sets were avail […]

library_books

Detection of two non synonymous SNPs in SLC45A2 on BTA20 as candidate causal mutations for oculocutaneous albinism in Braunvieh cattle

2017
PMCID: 5628493
PMID: 28982372
DOI: 10.1186/s12711-017-0349-7

[…] on of a possible pleiotropic effect of one or both mutations. Possible pleiotropy is, at this stage, highly speculative, but we would like to draw the attention to the fact that according to the EMBL-EBI Expression Atlas [], a low expression of the SLC45A2 gene is observed in bovine muscles, too. Analogous to Irion et al. [], the effects of both mutations could be tested with the help of the CRISP […]

library_books

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data

2017
PLoS Genet
PMCID: 5628936
PMID: 28945760
DOI: 10.1371/journal.pgen.1007001

[…] ogR) SNP probes with no reads at A and B alleles or with a BAF of 1 or 0 were removed. Using the SNP6 array probe positions for WGS data with ASCAT is a common approach, used successfully in the ICGC pancancer analysis of whole genomes project (https://dcc.icgc.org/pcawg) []. A wrapper program for ease of use is available []. […]

Citations

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PCAWG institution(s)
European Molecular Biology Laboratory,Hinxton, UK; ETH Zurich, Zurich, Switzerland, [etc]

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