TNBCtype

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]