Computational protocol: Preclinical evaluation of cyclin dependent kinase 11 and casein kinase 2 survival kinases as RNA interference targets for triple negative breast cancer therapy

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Protocol publication

[…] IHC scores for the CDK11 signal on human breast cancer arrays were determined by two independent observers. The average value was taken for each sample. The comparison between normal tissue and TNBC was conducted using a Wilcoxon rank-sum test and the median and range for each are reported. Mean immunoblot protein levels, cell viability values, and the number of clonal survival colonies were summarized and compared by treatment group using analysis of variance (ANOVA). The mean ± standard deviation is presented unless otherwise indicated. Mouse tumor volumes on days 7, 9 and 10 (relative to day 1) and primary tumor weights were summarized and compared by treatment group using ANOVA. P values for pairwise comparisons for the above analyses were conservatively adjusted for multiple comparisons using a Bonferroni correction. Differences between mouse weights on day 10 were compared by treatment group using paired t tests. The percentage of Ki67-positive cells was compared by treatment using ANOVA, adjusting for repeated measures within mice. Least-squares means ± standard errors are presented. P values for these comparisons with the control group were adjusted for multiple comparisons using Dunnett’s method.TCGA breast cancer RSEM-normalized read count RNASeq (v.2, level 3) data were downloaded from The Cancer Genome Atlas data portal (November 2014) and associated metadata (PAM50 RNAseq calls, sample type data) were downloaded from the UCSC Cancer Genome Browser (November 2014). Log2-transformed RSEM normalized read counts were used as the final gene expression measurement. ANOVA and Student t tests were used to test for differences in expression for seven genes between basal breast cancer subtype and normal or other subtype primary tumors. P values for pairwise comparisons were conservatively adjusted for multiple comparisons using a Bonferroni correction. P <0.05 values are reported and considered statistically significant for all analyses. […]

Pipeline specifications

Software tools RSEM, Array Suite
Databases TCGA Data Portal
Applications RNA-seq analysis, Genome data visualization
Organisms Mus musculus, Homo sapiens
Diseases Breast Neoplasms, Neoplasms