TNBCtype protocols

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TNBCtype specifications

Information


Unique identifier OMICS_19773
Name TNBCtype
Alternative name Triple-Negative Breast Cancer type
Interface Web user interface
Restrictions to use None
Input data Gene expression values.
Input format CSV
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Jennifer Pietenpol <>
  • person_outline Xi Chen <>

Additional information


http://cbc.mc.vanderbilt.edu/tnbc/help.php

Publication for Triple-Negative Breast Cancer type

TNBCtype in pipelines

 (2)
2017
PMCID: 5430301
PMID: 28555173
DOI: 10.3389/fonc.2017.00094

[…] the mutations in p53 occurring in cu_tnbc_005 and cu_tnbc_004 are frameshift and early termination mutations, respectively, and presumably also result in impaired p53 transactivation capacity. using tnbctype, cu_tnbc_002 and cu_tnbc_005 were predicted to represent the lar and mesenchymal (m) subtype, respectively. cu_tnbc_004 gene expression analysis using tnbctype was inconclusive and predicted […]

2016
PMCID: 4991491
PMID: 26980748
DOI: 10.18632/oncotarget.8014

[…] union mode with all other parameters set to default values. the resulting gene-by-sample matrix consisted of 12 er+ luminal b and 10 btnbc samples. tnbc subtypes listed in were predicted using tnbctype [] with fpkm expression values as input. differentially expressed genes (|log2fc| > 1.5 and fdr < 0.05) were identified with deseq2 [] using the same protocol applied to the pdx […]


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TNBCtype in publications

 (21)
PMCID: 5913636
PMID: 29365031
DOI: 10.1093/annonc/mdy024

[…] the molecular taxonomy of breast cancer international consortium (metabric) and the cancer genome atlas. tnbc samples (n = 550) were classified according to lehmann’s molecular subtypes using the tnbctype online subtyping tool (http://cbc.mc.vanderbilt.edu/tnbc/)., each subtype showed significant clinic-pathological characteristic differences. using a multivariate model, im subtype showed […]

PMCID: 5696233
PMID: 29190967
DOI: 10.18632/oncotarget.21669

[…] tnbc gene expression (rnaseq) data for primary tumors were obtained from the cancer genome atlas (tcga) [] via extraction from the ucsc cancer genome browser []. for each patient sample, the tnbctype webtool [] was used to classify that sample into the subtype according to lehmann et al []. differential gene expression analysis (dgea) was performed in r [] where one tnbc patient subtype […]

PMCID: 5604131
PMID: 28943920
DOI: 10.3892/ol.2017.6692

[…] of patients with tnbc achieved pcr in the neoadjuvant setting and the response of tnbc to chemotherapy was heterogeneous (,–). masuda et al () reported that lehmann's six gene expression subtypes (tnbctype) were associated with pcr status, with the bl1 subtype presenting a high rate of pcr (52%) compared with the m, im, msl and lar subtypes, which presented relatively low pcr rates (31, 30, 23 […]

PMCID: 5642571
PMID: 29050296
DOI: 10.18632/oncotarget.19719

[…] analysis, allows investigation of potential targets at the functional protein level,. we identified tnbc subtypes at the protein level using rppa and compared them with mrna molecular subtypes (tnbctype, tnbctype-4, and pam50) that is unique in its availability of both rppa and mrna analyses., we classified the samples from 80 tnbc patients using both k-means and hierarchical consensus […]

PMCID: 5430301
PMID: 28555173
DOI: 10.3389/fonc.2017.00094

[…] and performed 1,000 gene-set permutations to determine p-value. pathways with p < 0.05 were considered significant from the analysis., to predict the tnbc subtypes of the pdx models, we used the tnbctype web tool (http://cbc.mc.vanderbilt.edu/tnbc) (). rna-seq data for these models were uploaded to the tnbctype web tool. based on the gene expression profiles, the tnbctype was assigned […]


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TNBCtype institution(s)
Department of Biostatistics, Vanderbilt University, Nashville, TN, USA; Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
TNBCtype funding source(s)
Supported by NIH grants CA068485; CA95131 (Specialized Program of Research Excellence in Breast Cancer); CA148375; CA105436; CA070856; CA009385; American Cancer Society Grant #PF-10-226-01-TBG; and Komen Foundation grant SAC110030.2.0

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