Additional file 10 of Changes in correlation between promoter methylation and gene expression in cancer

Hierarchical clustering of breast cancer patients based on the average methylation level of CGI + SS associated with cluster 3down. (PDF 379 kb

Comparison of classification methods for clonality between pairs in the PT/LR cohort.

<p><b>Cor</b> (Correspondence): correspondence number with the Bollet/Servant cohort. <b>scores</b>: scores obtained with partial identity (PIS) or methylation (MS). <b>Time</b>: time elapsed between diagnosis of the PT and diagnosis of the recurrence. <b>Classification</b>: classification of the recurrence based on copy number (PIS), methylation (MS) or clinical features (clinical). <b>Divergence</b>: which method deviated from the others.</p

Histogram of the distribution of methylome-similarity score (MS) between unrelated PT/LR pairs.

<p>MS score for matched pairs is represented by circles. The vertical dashed line corresponds to the 95% quantile of the distribution of the MS scores for the unrelated pairs, used as a threshold to define clonal pairs ().</p

Correlation between methylation and copy-number scores.

<p>The horizontal red line (resp. vertical dashed blue line) corresponds to the 95% quantile of the distribution of the methylation-scores (resp. partial identity scores) for the unrelated pairs: (resp. ). PT/AM (resp. PT/LR, resp. PT/CL) pairs are colored in yellow (resp. blue, resp. pink). The black line corresponds to the linear regression between methylation and copy-number scores for all the datasets.</p

Lymphocytic infiltration in breast tumors.

<p><b>A</b> and <b>B:</b> Tumor specimen with weak lymphocytic infiltration (A: zoom x10 B: zoom x 40). Abbreviations: S = stroma, T = tumor, L = lymphocytes. Intratumoral TILs are indicated by a black star. <b>C</b> and <b>D</b>: Tumor specimen with prominent lymphocytic infiltration. (C: zoom x10 D: zoom x 40). Abbreviations: S = stroma, T = tumor, L = lymphocytes. Intratumoral TILs are indicated by a black star; stromal TILs are indicated by a blue star.</p

Summarized PT/LR Clinical and histological features.

<p><b>Cor</b> (Correspondence): correspondence number with the Bollet/Servant cohort from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103986#pone.0103986-Bollet1" target="_blank">[16]</a>, <b>Type</b>: histological type of the tumor (D =  ductal, L =  lobular), <b>Grade</b>: Aggressiveness of the tumor (1 to 3), <b>ER</b>: presence of estrogen receptors, <b>PR</b>: presence of progesterone receptors, <b>HER2</b>: presence of HER2 receptors, <b>Loc</b> (Location): 1 if the recurrence was located less than 4cm from the PT.</p

Pairwise methylome distance for each samples.

<p>Each boxplot represents the Manhattan distance between primary tumor and an unrelated locoregional evolution, or the Manhattan distance between locoregional evolution i and an unrelated primary tumor. The black square represent the Manhattan distance between the matched primary tumor and locoregional evolution from sample . The yellow (resp. blue, resp. pink) panel represents the PT/AM (resp. PT/LR, resp. PT/CL) set. The last panel represents the distribution of distances between the healthy breast tissue and all the other healthy breast tissues from the cohort.</p

Association between tumor-infiltrating lymphocyte levels and Immunity metagene expression in the REMAGUS dataset.

<p><b>A:</b> Percentage of intratumoral TILs according to Immunity metagene status (low <i>versus</i> high). <b>B</b> Percentage of stromal TILs according to Immunity metagene status (low <i>versus</i> high). <b>C</b>: Correlation between metagene expression and the percentages of intratumoral TILs. <b>D</b>: Correlation between metagene expression and the percentage of stromal TILs.</p

Distribution of methylation distances between different samples pairs for each groups.

<p><b>Real</b>: boxplot of methylome distances for all matched pairs that is a PT and its corresponding metastasis or recurrence. <b>Artificial</b>: boxplot of methylome distances for all unmatched pairs that is a PT and an unrelated metastasis or recurrence. <b>Primary</b>: boxplot of methylome distances to distances between two PT of two different individuals. <b>Recurrence</b>: boxplot of methylome distances between two metastasis or recurrence samples of two different individuals.</p

Significantly differentially methylated genes between PT and AM samples.

<p><b>CpG</b>: CpG probe name. <b>Gene</b>: Associated gene. <b>Pvalue</b>: FDR corrected p-value. <b>Methylation Variation</b>: Mean variation of methylation from the primary tumor to the axillary metastasis.</p