Table 1.
PIP and hormonal receptor status in breast cancer cell lines.
Figure 1.
PIP expression analysis after DHT treatment in breast carcinoma cell lines and normal mammary gland.
Relative abundance of PIP mRNA was assessed by Northern Blot analysis (upper panels). Total RNAs were extracted from normal mammary gland (MG, 15 µg) and from three breast carcinoma cell lines (MCF7, T47D and VHB1, 50 µg), at several days (0, 6, 8 and 10 days) after DHT treatment. The relative β-actin expression levels in each sample are shown (lower panels).
Table 2.
Statistical power simulations of the gene expression dataset.
Table 3.
False discovery rate of the gene expression dataset.
Figure 2.
Range of biological variability of the gene expression dataset.
Similarity dendrograms (Pearson correlation) resulting from unsupervised hierarchical clustering of DHT-treated (J7) or -untreated (J0) breast carcinoma cells based on the global gene expression matrix. [PIP+] and [PIP−] cells are indicated in red and blue, respectively.
Figure 3.
Hierarchical clustering of the differentially expressed genes.
Unsupervised hierarchical clustering of all samples for the genes found significantly differentially expressed (L235) between [PIP+] and [PIP−] phenotypes, and modulated in relation with the PIP expression. Genes (row) and samples (columns) are clustered independently using uncentered Pearson correlation metrics. [PIP+] and [PIP−] cell lines are indicated in red and green, respectively. The top-ranked relevant gene clusters (NODE 167X, NODE 196X and NODE 222X) selected using t-statistics with permutation-based adjustment (n = 10,000; α = 0.05) are indicated by color bars. The presence of the PIP gene is pointed.
Table 4.
Descriptive list of the genes selected for biological validation by quantitative RT-PCR (Q-PCR).
Table 5.
Q-PCR validation of the expression of the 41 selected genes in cell lines.
Table 6.
Functional analysis of PIP co-modulated genes.
Table 7.
Global network analysis of differentially expressed genes.
Figure 4.
Master molecular network of genes co-modulated with PIP.
Master network assembled by merging networks 1, 4 & 6 and networks 7, 8 & 10 identified by the IPA tool (version 4.0) from up- and down-regulated gene analysis using overlapping genes (cf. Table 7). The network is displayed graphically as nodes (genes/gene products) and edges (the biological relationship between the nodes). The [PIP+] relative to[PIP−] over-expressed genes are shaded in light red and down-regulated genes in green. The genes connected with PIP (EGR2 and CD4) and STAT5B, which was identified by a promoter analysis as a potential key regulator of the master network, are shaded in yellow. The nodes are represented using various shapes that represent the functional class of the gene products. Highly interconnected nodes (‘hub genes’) are moved to the network periphery together with the PIP gene. The hub genes belonging to L235 are shaded in gray and those, which were detected by quantitative PCR, are underlined. The gene names are written in green (down-regulated) or in red (up-regulated) relative to a [PIP+] versus [PIP−] modulation. An asterisk refers to a gene that was not selected in L235, but was identified at another level of the statistical analysis (* for L578&L2231 and ** for L1114 & L2231, Table S1).