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Additional file 3 Figures S1–S30. Supplementary figures.

Additional file 3. Methods: This file describes normal plasma cells purification, myeloma cells purification, 5mC and 5hmC dosage by mass spectrometry, bioinformatics methods and statistical analysis.

Additional file 2. Table S1: Patients characteristics, survival and mass spectrometry quantification of 5hmC and 5mC. Table S2: Scoring of 1816 5hmC-enriched domains across NDMM samples. Table S3: Motif analysis of core regulatory circuitries. Table S4: Scoring of groups-specific 5hmC-enriched domains. Table S5: Differential 5hmC-enriched domains between at diagnosis and relapse (DiffBind analysis).

GO biological process enrichment analyses of most differentially expressed genes between AG1 and AG3. Head of columns represents SAM gene lists used as ToppGene inputs. The ten first significant biological processes are displayed (cutoff p-value = 0.01). (PDF 45 kb)

Continuous GES analyses interpretation in function of ER status in the three age groups. (PDF 75 kb)

Continuous GES analyses interpretation in function of ER status in the three age groups. (PDF 75 kb)

Number of GO enrichment terms (biological tree) in common between GES’s gene lists. (PDF 68 kb)

GES listing, methods and references. (PDF 114 kb)

Percentage of GO enrichment terms (biological tree) in common between GES’s gene lists, sorted in decreasing order. (PDF 99 kb)

Metastasis-free survival (MFS) and overall survival (OS) analyses. MFS: 2A1: whole cohort; 2A2: Caucasian cohort. OS: 2B1: whole cohort; 2B2: Caucasian cohort. (PDF 230 kb)

Percentage of GO enrichment terms (biological tree) in common between GES’s gene lists, sorted in decreasing order. (PDF 99 kb)

Metastasis-free survival (MFS) and overall survival (OS) analyses. MFS: 2A1: whole cohort; 2A2: Caucasian cohort. OS: 2B1: whole cohort; 2B2: Caucasian cohort. (PDF 230 kb)

Number of genes in common between GES. (PDF 46 kb)

Number of genes in common between GES. (PDF 46 kb)

Number of GO enrichment terms (biological tree) in common between GES’s gene lists. (PDF 68 kb)

GES analyses differentiating AG1 and AG3 luminal B patients. AG1 > AG3 means that AG1 GES score is superior to AG3 GES score, and inversely. (PDF 57 kb)

GO biological process enrichment analyses of most differentially expressed genes between AG1 and AG3. Head of columns represents SAM gene lists used as ToppGene inputs. The ten first significant biological processes are displayed (cutoff p-value = 0.01). (PDF 45 kb)

GES scoring of breast cancer in function of age. Correlation matrices show Pearson correlation coefficients between continuous GES (red indicates a positive correlation; blue, a negative correlation) and dendrograms show mutual relationships of all signatures (scores were used for average-link hierarchical clustering using the Pearson correlation as a distance metric). 2A1: AG1, whole cohort; 2A2: AG2, whole cohort; 2A3: AG3 whole cohort; 2B1: AG1, Caucasian cohort; 2B2: AG2, Caucasian cohort; 2B3: AG3, Caucasian cohort. (PDF 1689 kb)

GES analyses differentiating AG1 and AG3 luminal B patients. AG1 > AG3 means that AG1 GES score is superior to AG3 GES score, and inversely. (PDF 57 kb)

GES scoring of breast cancer in function of age. Correlation matrices show Pearson correlation coefficients between continuous GES (red indicates a positive correlation; blue, a negative correlation) and dendrograms show mutual relationships of all signatures (scores were used for average-link hierarchical clustering using the Pearson correlation as a distance metric). 2A1: AG1, whole cohort; 2A2: AG2, whole cohort; 2A3: AG3 whole cohort; 2B1: AG1, Caucasian cohort; 2B2: AG2, Caucasian cohort; 2B3: AG3, Caucasian cohort. (PDF 1689 kb)