Figure 1
Pairwise correlation plots and SAM analyses heat maps. Samples were clustered based on pairwise correlation of gene expression profiles and are displayed based on a color gradient ranging from deep blue for a negative correlation to vivid red for a positive correlation. A negative correlation between 2 samples indicates that the genes used in the analysis have opposite expression tendencies (high/low). To the left of each correlation plot, a heat map showing the results from the SAM analysis is presented. Results are shown as an increasing green to red gradient representing the expression level. (A) Unsupervised clustering of AML-M0 with 253 AML samples of other subtypes and 3 CD34 sorted normal samples and corresponding SAM analysis (cutoff: 8-fold; 3472 probe sets). A dotted line delimits the AML-M0 samples within the overall AML-M0 cluster. The first column to the right of the correlation plot refers to the major mutation group the samples belong to and patients belonging to cluster no. 1018 (dark blue: cluster no. 10; yellow: t(15;17); gray: t(8;21); light blue: CEBPA mutation; dark red: inv(16); dark green: NPM1 mutations). The second column indicates the AML-M0 patients (in black) and CD34+ samples (in blue). The last column refers to the mutation status of RUNX1 in the AML-M0 samples. Mutations expected to lead to complete loss of function of RUNX1 are red and heterozygous mutations outside the runt domain are blue. In all 3 columns, green represents either a negative result for the variable(s) or no information available. (B) Unsupervised cluster analyses of all 35 AML-M0 samples and SAM analysis comparing groups A and B (cutoff: 9-fold; 1327 probe sets). Unsupervised clustering shows a strong correlation between samples with RUNX1 mutation, a tendency also evident in panel A. The first column to the left of correlation plot shows the status of the RUNX1 mutation as in panel A. The second column shows the mutation status for ETV6, blue representing a translocation involving this gene, whereas orange shows point mutations or insertions.13 In the third column, different detected mutations leading to a proliferative advantage (class I Mut) are represented in red (these include mutation of RAS, PTPN11, FLT3, and JAK2). The fourth column provides cytogenetic information. Trisomy 13, represented in yellow, is correlated to RUNX1 mutation.23,24 Blue stands for a normal karyotype; black, for a complex karyotype (more than 5 abnormalities). The last 2 columns represent expression levels for BLNK and TDT in all samples in which the histograms are proportional to the level of expression (probe set BLNK: 207655_s_at and TDT: 210487_at). In all columns, green represents either a negative result for the variable(s) or no information available.

Pairwise correlation plots and SAM analyses heat maps. Samples were clustered based on pairwise correlation of gene expression profiles and are displayed based on a color gradient ranging from deep blue for a negative correlation to vivid red for a positive correlation. A negative correlation between 2 samples indicates that the genes used in the analysis have opposite expression tendencies (high/low). To the left of each correlation plot, a heat map showing the results from the SAM analysis is presented. Results are shown as an increasing green to red gradient representing the expression level. (A) Unsupervised clustering of AML-M0 with 253 AML samples of other subtypes and 3 CD34 sorted normal samples and corresponding SAM analysis (cutoff: 8-fold; 3472 probe sets). A dotted line delimits the AML-M0 samples within the overall AML-M0 cluster. The first column to the right of the correlation plot refers to the major mutation group the samples belong to and patients belonging to cluster no. 1018  (dark blue: cluster no. 10; yellow: t(15;17); gray: t(8;21); light blue: CEBPA mutation; dark red: inv(16); dark green: NPM1 mutations). The second column indicates the AML-M0 patients (in black) and CD34+ samples (in blue). The last column refers to the mutation status of RUNX1 in the AML-M0 samples. Mutations expected to lead to complete loss of function of RUNX1 are red and heterozygous mutations outside the runt domain are blue. In all 3 columns, green represents either a negative result for the variable(s) or no information available. (B) Unsupervised cluster analyses of all 35 AML-M0 samples and SAM analysis comparing groups A and B (cutoff: 9-fold; 1327 probe sets). Unsupervised clustering shows a strong correlation between samples with RUNX1 mutation, a tendency also evident in panel A. The first column to the left of correlation plot shows the status of the RUNX1 mutation as in panel A. The second column shows the mutation status for ETV6, blue representing a translocation involving this gene, whereas orange shows point mutations or insertions.13  In the third column, different detected mutations leading to a proliferative advantage (class I Mut) are represented in red (these include mutation of RAS, PTPN11, FLT3, and JAK2). The fourth column provides cytogenetic information. Trisomy 13, represented in yellow, is correlated to RUNX1 mutation.23,24  Blue stands for a normal karyotype; black, for a complex karyotype (more than 5 abnormalities). The last 2 columns represent expression levels for BLNK and TDT in all samples in which the histograms are proportional to the level of expression (probe set BLNK: 207655_s_at and TDT: 210487_at). In all columns, green represents either a negative result for the variable(s) or no information available.

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