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TCGA Mbatch specifications

Information


Unique identifier OMICS_28409
Name TCGA Mbatch
Alternative name TCGA Batch Effects
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Documentation


TCGA Mbatch citations

 (6)
library_books

Circumvent the uncertainty in the applications of transcriptional signatures to tumor tissues sampled from different tumor sites

2017
Oncotarget
PMCID: 5444741
PMID: 28427173
DOI: 10.18632/oncotarget.15754

[…] A, http://cancergenome.nih.gov/), as described in detail in Table . The MBatch expression profiles with batch effects adjustment for two cancers types (colon and breast cancer) were download from the TCGA MBatch Web Portal (http://bioinformatics.mdanderson.org/tcgambatch/) [] and the clinical information for each sample was downloaded from the TCGA data portal, they were used to detected the genes […]

library_books

Gene Expression Differences in Prostate Cancers between Young and Old Men

2016
PLoS Genet
PMCID: 5189936
PMID: 28027300
DOI: 10.1371/journal.pgen.1006477

[…] oups (procedure described in ) and identified 24 samples in each age group (see for clinical characteristics of those selected samples). Batch-effect-removed mRNA sequence data were downloaded using TCGA MBatch web tool []. A two-sample t-test was performed to identify DEGs between the two tumor age groups. In addition, we specifically looked at expression levels of genes with outlying expression […]

library_books

Integrative modelling of tumour DNA methylation quantifies the contribution of metabolism

2016
Nat Commun
PMCID: 5171841
PMID: 27966532
DOI: 10.1038/ncomms13666

[…] We used the TCGA Batch Effects online tool (http://bioinformatics.mdanderson.org/tcgabatcheffects) to check for the existence of batch effects in the data used in our study. For each cancer types in our study, bo […]

library_books

Identification of MicroRNAs as Breast Cancer Prognosis Markers through the Cancer Genome Atlas

2016
PLoS One
PMCID: 5154569
PMID: 27959953
DOI: 10.1371/journal.pone.0168284

[…] Two gene expression profiles—RNA-Seq HiSeq V1 and V2—were downloaded from TCGA data portal. The two RNA-Seq datasets were investigated for batch effects with the TCGA Batch Effects Tool developed by MD Anderson Cancer (http://bioinformatics.mdanderson.org/tcgabatcheffects), which utilizes batch IDs to generate the Dispersion Separability Criterion (DSC); highe […]

library_books

RMEL3, a novel BRAFV600E associated long noncoding RNA, is required for MAPK and PI3K signaling in melanoma

2016
Oncotarget
PMCID: 5095033
PMID: 27167340
DOI: 10.18632/oncotarget.9164

[…] SKCM) project were downloaded from the Cancer Genomics Hub (CGHub) []. MD Anderson MBatch batch effects portal (http://bioinformatics.mdanderson.org/main/TCGABatchEffects:Overview) was used to verify TCGA Batch effects and no RNAseq significant batch effects were found.To compare expression levels, we used the transcripts per million (TPM) [] results of RSEM. Melanocytes sequencing read data (GSE3 […]

library_books

Functional annotation of colon cancer risk SNPs

2014
Nat Commun
PMCID: 4200523
PMID: 25268989
DOI: 10.1038/ncomms6114

[…] ned if any of the 182 genes show a significant increase or decrease (greater than twofold change and P-value <0.01) in colon tumours versus normal colon (see Methods and for an analysis of potential TCGA batch effects). We then eliminated those genes whose expression change did not correspond to the nature of the enhancer (for example, a tumour-specific enhancer should not regulate a gene that is […]

Citations

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TCGA Mbatch funding source(s)
Supported by Grant number U24CA143883 from NCI/NIH, the Michael & Susan Dell Foundation: the Lorraine Dell Program in Bioinformatics for Personalization of Cancer Medicine, the H.A. & Mary K. Chapman Foundation and anonymous donor for Computational Biology in Cancer Medicine.

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