Supplementary File S1 - Springer Static Content Server

Supplementary File S1 - Tables of alteration for selected gene sets and gene families

CAN-genes Breast cancer CAN-genes with significant gains or losses and showing significant up or downregulation of expression. Columns label the chromosome (CHR), the frequency of gain and loss (Freq.Gain & Freq.Loss), whether the expression association (Expr) is between copy-number gain and overexpression (G) or copynumber loss and underexpression (L), and the p-value of significance as determined by the Wilcoxon rank sum test (pval). Name ABCB10 NCOA6 NUP133 OBSCN PPM1E C22orf19 DDX10 GGA1 SORL1

CHR 1 20 1 1 17 22 11 22 11

Freq.Gain 0.56725 0.26316 0.56725 0.54678 0.19298 0.05848 0.04678 0.06433 0.04094

Freq.Loss 0.0117 0.00585 0.0117 0.0117 0.05263 0.19298 0.22807 0.22807 0.22807

Expr G G G G G L L L L

pval < 10−4 < 10−4 < 10−4 < 10−4 0.06 0.0006 0.001 0.06 0.04

The phosphatome Phosphatases with significant gains or losses and showing significant up or downregulation of expression. Columns label the chromosome (CHR), the frequency of gain and loss (Freq.Gain & Freq.Loss), whether the expression association (Expr) is between copy-number gain and overexpression (G) or copy-number loss and underxpression (L), and the p-value of significance as determined by the Wilcoxon rank sum test (pval). Name PTPRA PTPRC DUSP10 DUSP12 DUSP15 PTP4A3 MTMR4 PTPRK MTMR2 EYA4

CHR 20 1 1 1 20 8 17 6 11 6

Freq.Gain 0.22807 0.54971 0.55556 0.55556 0.25146 0.45029 0.18713 0.09357 0.07018 0.08772

Freq.Loss 0.02339 0 0 0.00585 0.00585 0.07018 0.05263 0.15497 0.19883 0.15205

Expr G G G G G G G L L L

1

pval 0.003 0.09 0.098 0.0002 0.008 0.08 0.06 0.02 0.02 0.05

Histones and Chromatin Modifiers Histones and chromatin modifiers with significant gains or losses and showing significant up or downregulation of expression. Columns label the chromosome (CHR), the frequency of gain and loss (Freq.Gain & Freq.Loss), whether the expression association (Expr) is between copy-number gain and overexpression (G) or copy-number loss and underxpression (L), and the p-value of significance as determined by the Wilcoxon rank sum test (pval). Abbreviations: histone methyltransferase (HMT), helicase (HELIC), histone acetyltransferase (HAT), histone deacetyltransferase (HDAC), histone (HIST), histone demethyltransferase (HDMT), bromodomain associated (BROM.DOM), chromatin assembly (CHROM.ASSEM.), chromatin domain associated (CHROM.DOM).

2

Name ARID4B ADA ASH2L CHAF1B CHD1L / POLR3C CHRAC1 CREBBP DNMT3B FBXO18 FKBP1A H2AFV H3F3B HDAC2 HIST1H1B HIST1H1D HIST1H2BD HIST1H2BE HIST1H2BI HIST1H3C HIST2H2AA HIST2H4 JARID1B / CYB5R1 JMJD1B L3MBTL MYST1 PARP1 RBBP6 SETDB1 SMYD3 SUV39H2 THEX1 THRAP4 UBE2D2 UBE2V2 WHSC1L1 BRD1 CHAF1A CHD9 EP300 H1F0 MBD2 MIZF MLL NCOR1 / TTC19 NHP2L1 PRMT7 SAP18 SIRT3 SLBP UBE2G1 UBE2L3

Type HDMT HMT HELIC HAT HELIC

HDAC HIST HIST HIST HIST HIST HIST HIST HIST HDMT HDMT HAT

HMT HMT HMT

HMT BROM.DOM CHROM.ASSEM. CHROM.DOM HAT HIST MBD2-interact. HMT HDAC-complex HMT HDAC-complex HDAC

CHR 1 20 8 21 1 8 16 20 10 20 7 17 6 6 6 6 6 6 6 1 1 1 5 20 16 1 16 1 1 10 8 17 5 8 8 22 19 16 22 22 18 11 11 17 22 16 13 11 4 17 22 3

Freq.Gain 0.55166 0.26901 0.31579 0.10526 0.49269 0.50292 0.33333 0.24561 0.20468 0.23392 0.12865 0.16959 0.09357 0.12865 0.1345 0.1345 0.1345 0.1345 0.1345 0.52047 0.51901 0.57018 0.10526 0.26316 0.19883 0.55556 0.36842 0.53216 0.5731 0.21053 0.1345 0.16374 0.11111 0.35673 0.32164 0.05848 0.04094 0.07018 0.06433 0.07018 0.07602 0.03509 0.04094 0.02924 0.05848 0.02924 0.05263 0.02924 0.07018 0.04094 0.07018

Freq.Loss 0.0078 0.01754 0.14035 0.08187 0.00731 0.04094 0.07018 0.0117 0.01754 0.02339 0.04094 0.11111 0.1462 0.02924 0.02924 0.02924 0.02924 0.02339 0.02924 0.00585 0.01901 0.00877 0.07602 0.02924 0.20468 0 0.03509 0.0117 0.01754 0.01754 0.24561 0.07018 0.07602 0.04094 0.12865 0.23392 0.11696 0.34795 0.22807 0.22807 0.14035 0.24561 0.23977 0.25146 0.22807 0.4386 0.16959 0.15205 0.14035 0.2807 0.21637

Expr G G G (L) G G G G G G G G G G (L) G G G G G G G G G G G G G G G G G G G G G G L L L L L L L L L L L L L L L L

pval < 10−4 0.03 < 10−5 (0.04) < 10−4 0.02 0.08 0.03 0.006 0.05 0.08 0.006 < 10−5 0.0001 (0.04) 0.009 0.07 0.09 0.01 0.05 0.04 < 0.1 < 10−4 0.0003 0.06 0.005 0.05 < 10−5 0.03 0.003 0.09 < 10−5 0.08 0.0001 0.01 < 10−4 0.0007 0.04 0.05 0.01 0.03 0.03 0.0004 0.005 0.09 < 10−4 0.01 0.0002 0.0004 0.002 0.07 0.002 0.002

The Kinome Kinases with significant gains or losses and showing significant up or downregulation of expression. Columns label the chromosome (CHR), the frequency of gain and loss (Freq.Gain & Freq.Loss), whether the expression association (Expr) is between copy-number gain and overexpression (G) or copy-number loss and underxpression (L), and the p-value of significance as determined by the Wilcoxon rank sum test (pval). Name ATR CDK5 CLK2 HER2/ERBB2 GSK3B LIMK1 MARK1 PHKG1 TRIO DYRK3 RIPK2 MAPKAPK2 SGK2 BCKDK TLK2 ZC2/TNIK SGK3 PIK3R4 CDKL3 PBK SCYL3 OBSCN NEK7 ILK NEK3 MAP2K4 TESK1 RIOK3 STK33 MLKL PIM3 ULK3

CHR 3 7 1 17 3 7 1 7 5 1 8 1 20 16 17 3 8 3 5 8 1 1 1 11 13 17 9 18 11 16 22 15

Freq.Gain 0.18713 0.12281 0.50292 0.27485 0.16959 0.15789 0.55556 0.1345 0.21053 0.5731 0.48538 0.5731 0.26316 0.19298 0.23977 0.15497 0.42105 0.15789 0.11111 0.12865 0.54971 0.54678 0.54386 0.02924 0.02924 0.02339 0.08772 0.07602 0.02924 0.04094 0.05848 0.05848

Freq.Loss 0.02339 0.06433 0.02924 0.07018 0.02339 0.05263 0 0.02339 0.02924 0 0.01754 0 0.02924 0.20468 0.03509 0.02924 0.01754 0.01754 0.10526 0.27485 0.00585 0.0117 0.00585 0.12865 0.21053 0.26901 0.10526 0.12281 0.12281 0.4386 0.24561 0.09357

Expr G G G G G G G G G G G G G G G G G G G G G G G L L L L L L L L L

4

pval 0.002 0.09 < 10−4 < 10−5 0.08 0.03 0.08 0.04 0.02 0.06 < 10−4 0.008 0.005 0.07 0.02 0.003 0.04 0.01 0.001 0.01 < 10−4 < 10−4 0.09 0.03 0.002 0.0001 0.004 0.07 0.04 0.005 0.03 0.06