Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data

Table 1 Numerical analysis of massively parallel signature sequencing

	Malignant breast epithelium	Normal luminal epithelium
Sequence signatures	24,288	28,404
Uniquely mapped signatures	14,245	10,249
Unique HTR clusters	8,421 (3,191)^a	6,477 (1,297)^a
Dynamic range	<9,808 tpm	<35,847 tpm
Differentially expressed transcripts	4,311 T > L	2,242 L > T

Sequence signatures represent the total number of sequences obtained by massively parallel signature sequencing (MPSS). Uniquely mapped signatures correspond to the total number of human transcriptome clusters identified and retained in the 'gene-centric' annotation. Unique human transcriptome database (HTR) clusters are transcripts that mapped to a single human cluster and had an abundance of ≥3 transcripts per million (tpm) (approximately one transcript/cell). As described in Materials and methods, statistically significantly (P ≤ 0.05) differentially expressed transcripts were determined and separated into tumour (T) over normal luminal (L) or vice verse, depending on their fold change. ^aCorresponds to HTR clusters found in only one sample.

ISSN: 1465-542X