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Protocols

CGHub specifications

Information


Unique identifier OMICS_05807
Name CGHub
Alternative name Cancer Genomics Hub
Restrictions to use None
Maintained No

Taxon


  • Primates
    • Homo sapiens

Publication for Cancer Genomics Hub

CGHub citations

 (103)
library_books

Unifying cancer and normal RNA sequencing data from different sources

2018
Sci Data
PMCID: 5903355
PMID: 29664468
DOI: 10.1038/sdata.2018.61

[…] Raw paired-end reads of the RNA-seq samples for the TCGA project were retrieved from the Cancer Genomics Hub (CGHub, https://cghub.ucsc.edu). When FASTQ files were not available, e.g., for stomach adenocarcinoma, we downloaded aligned sequence reads (in BAM format) and extracted reads fro […]

library_books

Helicase like transcription factor expression is associated with a poor prognosis in Non Small Cell Lung Cancer (NSCLC)

2018
BMC Cancer
PMCID: 5902896
PMID: 29661164
DOI: 10.1186/s12885-018-4215-y

[…] tations in Cancer (http://cancer.sanger.ac.uk/cosmic; []).To obtain gene expression estimates for individual mRNA forms, paired-end RNAseq raw read data from the TCGA project were downloaded from the Cancer Genomics Hub (https://cghub.ucsc.edu/). In brief, reads were mapped to the latest human reference assembly, hg19, using TopHat, a splice-aware short-read aligner (http://ccb.jhu.edu/software/to […]

call_split

Correlation of gene expression and associated mutation profiles of APOBEC3A, APOBEC3B, REV1, UNG, and FHIT with chemosensitivity of cancer cell lines to drug treatment

2018
Hum Genomics
PMCID: 5896091
PMID: 29642934
DOI: 10.1186/s40246-018-0150-x
call_split See protocol

[…] We downloaded unprocessed WES BAM files, which were available for 325 CCLE cell lines (Fig. ), from the CCLE project at the National Cancer Institute (NCI) Cancer Genomics Hub; these data are available at the NCI Genomic Data Commons (GDC) data portal []. All CCLE WES data had been reported to be sequenced at the Broad Institute using the same version of […]

library_books

Novel therapeutic strategy for cervical cancer harboring FGFR3 TACC3 fusions

2018
Oncogenesis
PMCID: 5833787
PMID: 29358619
DOI: 10.1038/s41389-017-0018-2

[…] We downloaded TCGA RNA sequencing data obtained from 306 uterine cervical cancer samples from the Cancer Genome Hub (CGHub, https://cghub.ucsc.edu). We detected 445 high confidence fusion transcripts by using the Pipeline for RNA sequencing Data Analysis (PRADA). Of 306 TCGA cervical cancer samples, we identified fo […]

call_split

A RNA Sequencing approach for the identification of novel long non coding RNA biomarkers in colorectal cancer

2018
Sci Rep
PMCID: 5766599
PMID: 29330370
DOI: 10.1038/s41598-017-18407-6
call_split See protocol

[…] RNA-seq data for colon cancer (682 samples) as well as normal colon tissues (41 samples) were downloaded from Cancer Genomics Hub. Differential gene expression analysis was performed on this dataset to verify the differentially expressed genes found from 3-pair RNA-Seq dataset. Large sample size of TCGA datas […]

library_books

Punctuated evolution of canonical genomic aberrations in uveal melanoma

2018
Nat Commun
PMCID: 5760704
PMID: 29317634
DOI: 10.1038/s41467-017-02428-w

[…] Raw data files from 80 TCGA UM samples was obtained from the Cancer Genomics Hub (CGHub). Raw data files from the Martin et al. and Furney et al. raw data were obtained from the European Genome-phenome Archive (EGA). Data sets provided in BAM format (TCGA; Furn […]

Citations

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CGHub institution(s)
Biomolecular Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA, USA; Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA, USA; Annai Systems Inc, California, USA, Cardinal Peak, LLC, CO, USA; Information Technology Services, University of California Santa Cruz (UCSC), Santa Cruz, CA, USA

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