TNBCtype pipeline

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 pipeline

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

[…] 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 table s11b were predicted using tnbctype [53] with fpkm expression values as input. differentially expressed genes (|log2fc| > 1.5 and fdr < 0.05) were identified with deseq2 [54] using the same protocol applied to the pdx […]

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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