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Additional file 9: Figure S2. Scatter plots showing the relationship between chromosome arm imbalance scores in cancer (Cancer_AN) and normal gene expression (Normal_GE) for each tissue/tumor type.

Additional file 5: Figure S1. Scatter plots correlating chromosome arm imbalance scores (X axes) with arm-wide expression levels in cancer (upper row, Y axes) and normal tissue (lower row, Y-axes).

Additional file 1. Supplementary Tables: Table S1. Molecular subtypes of breast cancer cell lines. Table S2. Histopathological features of tissue microarray samples. Table S3. Clinical-pathological parameters and CBP & GCN5 expression in DCIS and breast carcinoma cases. Supplementary Figures: Fig. S1. Baseline expression level of ER and HER2 in a panel of normal cancer breast cells. Fig. S2. Efficiency of transfection kinetics for a, b HER2 siRNA, c-e ER siRNA and f, g both ER and HER2 siRNAs. Fig. S3. Efficiency of transfection kinetics for a, b CBP siRNA in MCF7 and T47D cells. Fig. S4. Uncropped blots for a CBP and b GCN5 proteins in normal and cancer breast cells. Fig. S5. Uncropped blots for HER2 and CBP proteins in a SkBr3 and b BT-474 cells transfected with HER2 siRNA for 24-96 hours. Fig. S6. Uncropped blots for CBP protein in a SkBr3 and b BT-474 cells treated with Trastuzumab for 24-96 hours. Fig. S7. Uncropped blots for ER and CBP proteins in a MCF7 and b T47D cells transfected with ER siRNA for 24-96 hours. Fig. S8. Uncropped blots for ER and CBP proteins in a BT-474 cells transfected with ER siRNA for 24-96 hours. Uncropped blots for CBP protein in b MCF7, c T47D and d BT-474 cells treated with Tamoxifen for 24-96 hours. Fig. S9. Uncropped blots for ER, HER2 and CBP proteins in a BT-474 cells transfected with ER and HER2 siRNAs for 24-96 hours. Uncropped blots for CBP protein in b BT-474 cells treated with Tamoxifen and Trastuzumab combination for 24-96 hours. Fig. S10. Uncropped blots for ER and CBP proteins in a MCF7 and b T47D cells transfected with CBP siRNA for 24-96 hours. Fig. S11. Kaplan-Meier survival curves of disease-free survival for CBP expression in a Luminal A, b Luminal B HER2 negative, c Luminal B HER2 positive, d HER2-positive and e Triple negative breast cancer patients. Fig. S12. Kaplan-Meier survival curves of disease-free survival for GCN5 expression in a Luminal A, b Luminal B HER2 negative, c Luminal B HER2 positive, d HER2-positive and e Triple negative breast cancer patients.

Additional file 10: Figure S3. Scatter plots showing the relationship between chromosome arm imbalance scores in cancer (Cancer_AN) and normal gene expression (Normal_GE) for each chromosome arm.

Figure S1. MALDI imaging intensity box plots of identified peptides for UBE2N (m/z 1043.635 & m/z 1203.593; top) and SPTBN1 (m/z 959.513 & m/z 1203.593 bottom). Intensity plots of the two identified peptides UBE2N and SPTBN1 detected differentially regulated by MALDI imaging. Figure S2. Tissue-microarray-based immunohistochemical evaluation of UBE2N by means of image scope comparing normal mucosa vs. CRC and euploid vs. aneuploid CRCs after combining data of the training and validation TMA set. Bar plots and ROC curve of immunhistochemical data of UBE2N after combining data of the training and validation TMA set. Figure S3. Exemplary immunohistochemical UBE2N stainings of the TMA validation set. Images are presented as an overview (A) as well as an image section (B). Overview of exemplary immuohistochemical images of UBE2N. The images present results from the TMA validation set. Figure S4. Tissue-microarray-based immunohistochemical evaluation of SPTBN1 by means of image scope comparing normal mucosa vs. CRC and euploid vs. aneuploid CRCs in the training and validation set. Bar plots of immunhistochemical data of SPTBN1. The images present results from the TMA validation set. (DOCX 21654 kb)

Additional file 11: Figure S4. Scatter plots depicting correlation of chromosome arm-wide gene expression levels in normal tissues based on the GTEx database with chromosome arm wide aneuploidies and corresponding chromosome arm-wide cancer gene expression levels in associated cancer types of 4 tissues (Kidney, Brain, Cervix and Colon).

Additional file 9: Figure S2. Scatter plots showing the relationship between chromosome arm imbalance scores in cancer (Cancer_AN) and normal gene expression (Normal_GE) for each tissue/tumor type.

Additional file 11: Figure S4. Scatter plots depicting correlation of chromosome arm-wide gene expression levels in normal tissues based on the GTEx database with chromosome arm wide aneuploidies and corresponding chromosome arm-wide cancer gene expression levels in associated cancer types of 4 tissues (Kidney, Brain, Cervix and Colon).