Table 3.

Step-by-step output as numbers of qualifying genes along the LSTNR analytical pipeline for RNAseq data deposited in TCGA from four realizations of patient-derived breast cancer transcriptomes across four molecular subtypes (courtesy of Li and Bushel, 2016; 10.1186/s12864-016-2584-7).

Criteria	Breast Cancer Molecular Subtypes (TCGA) (N = 200)
	Realization 1 (N = 50)	Realization 2 (N = 50)	Realization 3 (N = 50)	Realization 4 (N = 50)	All Specimens (N = 200)
Genes with uniquely aligned reads	20,532
Distribution of gene-wise RPM means	P(y) ~Weibull3P(y;α,ß,γ); y = RPM
	α = 25.4 RPM	α = 24.1 RPM	α = 25.0 RPM	α = 21.9 RPM	α = 22.2 RPM
	ß = 0.53	ß = 0.53	ß = 0.54	ß = 0.49	ß = 0.49
	γ = 9.9 × 10−3 RPM	γ = 6.6 × 10−3 RPM	γ = 1.1 × 10−2 RPM	γ = 1.6 × 10−3 RPM	γ = 1.5 × 10−3 RPM
Independent filtering: Genes with average y > α	8,005	8,110	8,083	8,562	8,538
Linearized normalizing transformant: GLM Linear Predictor	(y–γ)−1
Transformant two-way ANOVA: resolved genes across groups with respect to gene-wise mean	4,295	381	638	2,281	2,851
Resolution-Weighed ANOVA: Significant Genes (SGs) with FDR adj. p < 0.05 based on differences in resolution-weighed RPM log-fold changes (Log2FC) relative to baseline condition	4,465	5,086	4,537	4,618	6193
	Altogether: 7,749				Final Overlap: 1,509
	Intersection: 1,617
Differential expression: DEGs = subset of SGs that exhibit both: resolution-weighed effect size above 5% of gene-wise variation (δLog2FC > 0.3 × σSSR); and post-hoc pairwise-significant Log2FC differences between at least two groups (Student's t-test p < 0.05)	3,736	3,377	3,497	3,617	6,093
	Altogether: 6,407				Final Overlap: 908
	Intersection: 976
Reproducibility: LSTNRs = subset of SGs that exhibit both: resolution-weighed effect size above 5% of gene-wise variation (δLog2FC > 0.3 × σSSR); and at least one group with Log2FC differences vs. baseline greater than 95% Tolerance Interval of gene × group residuals among SGs (post-hoc pairwise-significance not required)	1,370	1,102	1,130	1,210	1,511
	Altogether: 2,193				Final Overlap: 337
	Intersection: 368
Expectable DEGs: DEGREEs = Ensembl-annotated DEGs with a reproducible expectation estimate (i.e., DEGs that are also LSTNRs) and official Entrez symbol	Intersection: 366				1,511
					Final Overlap: 336
Transcriptional profiling: Profiler DEGREEs = top DEGREEs ranked by retrospective statistical power with monotonically decreasing within-gene effect sizes ΔLog2FC	200 Profiler DEGREEs (consensus)
Diagnostic targets: Biomarkers = minimal subset of Profiler DEGREEs with predictive discriminant power based on sequential partition tree analysis (ROC scores > 0.9 per phenotype)	CBX7, ESR1, FOXC1, and FOXM1