www.sciencetranslationalmedicine.org/cgi/content/full/7/318/318ra202/dc1 Supplementary Materials for Therapeutic targeting of casein kinase 1 in breast cancer Laura H. Rosenberg, Marie Lafitte, Victor Quereda, Wayne Grant, Weimin Chen, Mathieu Bibian, Yoshihiko Noguchi, Mohammad Fallahi, Chunying Yang, Jenny C. Chang, William R. Roush, John L. Cleveland, Derek R. Duckett* The PDF file includes: *Corresponding author. E-mail: ducketdr@scripps.edu Published 16 December 2015, Sci. Transl. Med. 7, 318ra202 (2015) DOI: 10.1126/scitranslmed.aac8773 Fig. S1. CK1δ, but not CK1ε, is overexpressed in human breast cancer and associated with CSNK1D gene amplification. Fig. S2. CK1δ is overexpressed in human breast cancer specimens. Fig. S3. Silencing of CK1δ and CK1ε, but not CK1ε alone, impairs growth and survival of MDA-MB-231 breast cancer cells. Fig. S4. Selective inhibition of FLT3 has no effect on proliferation of MDA-MB- 231 breast cancer cells. Fig. S5. Treatment with SR-3029 impairs growth of triple-negative and HER2 + breast tumor models. Fig. S6. Long-term daily dosing with SR-3029 has no adverse effects on major organ histology. Fig. S7. Selective silencing of CK1δ is sufficient to impair growth of MDA-MB- 231 breast cancer cells. Fig. S8. Wnt/β-catenin pathway genes are a hallmark of CK1δ-expressing breast cancers. Fig. S9. Constitutively active β-catenin N90 rescues the growth inhibitory effects of CK1δ inhibition and silencing. Fig. S10. CK1δ expression in MCF7 breast cancer cells sensitizes them to SR- 3029. Fig. S11. Cyclin D1 expression is suppressed in TNBC MDA-MB-231 derived tumors after knockdown of CK1δ. Fig. S12. Inhibition of CK1δ/CK1ε has no effect on intestinal homeostasis. Fig. S13. Canonical Wnt signaling genes are correlated with CK1δ expression in human renal and bladder cancer.
Table S1. TCGA RNA-seq and GISTIC2 copy number data and correlation analysis for breast cancer (BRCA) tumors. Table S2. TCGA RNA-seq and GISTIC2 copy number data for basal-like Pam50 breast tumors. Table S3. TCGA RNA-seq and GISTIC2 copy number data for HER2-positive Pam50 breast tumors. Table S4. TCGA RNA-seq and GISTIC2 copy number data for luminal A Pam50 breast tumors. Table S5. TCGA RNA-seq and GISTIC2 copy number data for luminal B Pam50 breast tumors. Table S6. Potency of the CK1δ/CK1ε inhibitor SR-3029 for human breast cancer subtypes. Table S7. No toxic effects from long-term daily treatment with SR-3029. Table S8. TCGA RNA-seq and GISTIC2 copy number data for renal papillary (KIRP) tumors. Table S9. TCGA RNA-seq and GISTIC2 copy number data for bladder cancer (BLCA) tumors. Table S10. Renal papillary cell carcinoma correlation analysis. Table S11. Bladder cancer correlation analysis. Table S12. Wnt signaling genes significantly associated with CK1δ expression in renal papillary cell carcinoma. Table S13. Wnt signaling genes significantly associated with CK1δ expression in bladder cancer. Table S14. Oligonucleotides used for qpcr. Table S15. sirna sequences. Table S16. shrna sequences.
Supplementary Figures Fig. S1. CK1δ, but not CK1ε, is overexpressed in human breast cancer and associated with CSNK1D gene amplification. (A) CK1δ expression in 53 invasive breast carcinomas vs. normal breast tissue analyzed with Oncomine (14). (B) CK1ε expression in 392 invasive breast carcinomas (TCGA) vs. normal breast tissue analyzed with Oncomine. (C) Proportional frequency of CSNK1D copy number amplifications (high and low) by breast cancer subtype (TGCA; Basal, n=135, HER2+, n=67, Luminal A, n=413, Luminal B, n=192). (D) Scatter plots of
CSNK1D Log2 mrna expression vs. Log2 copy number values for each of the major Pam50 breast cancer subtypes.
Fig. S2. CK1δ is overexpressed in human breast cancer specimens. Immunohistochemical staining for CK1δ in normal breast tissue (top panels) and human breast carcinoma specimens (bottom panels) (www.proteinatlas.org). Nine out of the eleven tumors analyzed showed high expression of CK1δ. One representative core is shown for each patient s tumor (scale bar=400 μm).
Fig. S3. Silencing of CK1δ and CK1ε, but not CK1ε alone, impairs growth and survival of MDA- MB-231 breast cancer cells. (A) Immunoblot and qpcr analyses showing knockdown of CK1δ and CK1ε in MDA-MB-231 cells after transfection with either non-targeting (NT) sirnas or sirnas directed against both CK1δ and CK1ε (n=3; **, p=0.01). (B) Percentage of apoptotic cells
(left) measured by trypan blue exclusion (n=3; ***, p=0.0002) and relative growth (right) (n=3; ***, p=0.0003) 3 days after sirna transfection. (C) MDA-MB-231 cells were transiently transfected with expression vectors containing sirna-resistant cdna of either CK1δ or GFP 24 hours before transfection with sirnas. 3 days later, CK1δ expression was analyzed by immunoblot (top panel), and relative cell growth was determined by counting (bottom panel). (D) Selective knockdown of CK1ε in MDA-MB-231 cells after transfection with non-targeting (NT) sirnas or sirnas against CK1ε (n=3; ***, p<0.0001). (E) Percentage of apoptotic cells (left) and relative growth (right) 3 days after sirna transfection (n=3; ***, p<0.0001).
% DMSO Control EC 50 [M] SR-2890 2.397e-008 SR-1277 3.403e-008 140 120 100 80 AC220 SR-2890 SR-1277 60 40 20 0-10 -9-8 -7-6 -5-4 [M] Compound Fig. S4. Selective inhibition of FLT3 has no effect on proliferation of MDA-MB-231 breast cancer cells. Comparison of the anti-proliferative potency of AC220 (a FLT3 inhibitor) vs. SR- 2880 and SR1277 (close analogs of SR-3029) on MDA-MB-231 breast cancer cells. Data are plotted as % proliferation vs. vehicle (DMSO control) (n=3).
Fig. S5. Treatment with SR-3029 impairs growth of triple-negative and HER2 + breast tumor models. (A) Left, Caliper measurements of MDA-MB-231 tumor size in mice treated with vehicle or SR-3029. Treatment began at day 30 (20 mg/kg/day i.p.). Mean tumor volumes are shown for each cohort at day 35 vs. day 61, which demonstrates significant tumor regression (n=7 mice per cohort; **, p=0.01). Right, treatment of MDA-MB-468 tumors (20 mg/kg/day i.p.) began at day 42 after implantation (20 mg/kg/day i.p.). Graph shows mean tumor volume at day 42 vs. day 64 (n=8-9; ***, p=0.0006). (B) Caliper measurements of SKBR3 tumor growth in mice treated with vehicle or SR-3029. Treatment began at day 60 (20 mg/kg/day i.p.) and was terminated at day 96 due to the hemorrhagic nature of the vehicle-treated tumors.
Fig. S6. Long-term daily dosing with SR-3029 has no adverse effects on major organ histology. Mice were treated with vehicle or SR-3029 for 48 days (once daily, 20 mg/kg i.p.). The indicated tissues were then examined by H&E staining (representative images are shown, scale bar 200 microns).
Fig. S7. Selective silencing of CK1δ is sufficient to impair growth of MDA-MB-231 breast cancer cells. MDA-MB-231 cells expressing Dox-inducible non-targeting (NT) or CK1δ shrna were treated with 1 µg/ml Dox for 72 hours before transfection with CK1δ or GFP cdnaexpressing vectors resistant to shrna. After an additional 72 hours, CK1δ expression was analyzed by immunoblot (top panel), and relative cell growth was determined by counting (bottom panel) (n=4; **, p= 0.009).
Fig. S8. Wnt/β-catenin pathway genes are a hallmark of CK1δ-expressing breast cancers. (A) Heatmap of the CK1δ signature list (612 genes) in TCGA RNA-Seq breast cancer dataset. (B) Volcano Plot function showing differentially expressed genes in CK1δ-high versus CK1δ-low expressing tumors (from TCGA RNA-Seq breast cancer dataset). Corrected p value cut-off was
set to 0.05 and fold change cut-off was set to 2 to identify hits (red dots). (C) Wnt pathway genes differentially expressed (fold change) between CK1δ-high and CK1δ-low groups.
Fig. S9. Constitutively active β-catenin N90 rescues the growth-inhibitory effects of CK1δ inhibition and silencing. (A) MDA-MB-231 cells stably expressing the N90 β-catenin mutant or parental MDA-MB-231 cells were treated with or without 30 nm SR-3029 for 48 hours. Effects on cell growth (left) and apoptosis (right) were determined (n=3; *, p=0.02; ***, p=0.003). (B) Expression of nuclear endogenous β-catenin or the N90 β-catenin mutant in cells treated with the indicated concentrations of SR-3029. (C) Cell growth (left) and apoptosis (right) were measured after 5 days of Dox treatment (1 µg/ml) of MDA-MB-231-shCK1δ cells expressing the N90 β-catenin mutant or vector only MDA-MB-231 shck1δ cells (n=3; left to right, *** p=0.0003 and 0.0002).
Fig. S10. CK1δ expression in MCF7 breast cancer cells sensitizes them to SR-3029. (A) Immunoblot showing relative expression of nuclear and cytoplasmic β-catenin in MDA-MB-231 vs. MCF7 cells. Experiment shown is representative of 3 independent experiments. (B) Growth of MCF7-CK1δ vs. MCF7-GFP cells measured over 72 hours with the indicated concentrations of SR-3029 (n=3; **, p=0.01; ***, p=0.005).
Fig. S11. Cyclin D1 expression is suppressed in TNBC MDA-MB-231 derived tumors after knockdown of CK1δ. (A) qpcr showing CK1δ knockdown and reduced Cyclin D1 mrna expression in MDA-MB-231-derived tumors after 7 days of Dox (administered ad lib in chow, 200 mg/kg) (n=3 mice; *, p=0.023. ***, p=0.003). (B) Left, down-regulation of Cyclin D1 protein after knockdown of CK1δ in MDA-MB-231-derived tumors from mice treated as above. Right, quantification of B, normalized to GAPDH (*, p=0.028).
A Vehicle SR-3029 B DAPI TUNEL Vehicle SR-3029 Fig. S12. Inhibition of CK1δ/CK1ε has no effect on intestinal homeostasis. (A) H&E stained small intestine tissue sections and (B) TUNEL staining of cryosections prepared from mice treated with vehicle or SR-3029 (once daily, 20 mg/kg i.p.) for 48 days (representative images are shown; scale bar 200 microns).
Fig. S13. Canonical Wnt signaling genes are correlated with CK1δ expression in human renal and bladder cancer. Heatmaps derived from the indicated TCGA RNA-Seq datasets showing expression of Wnt pathway genes in CK1δ-high vs. CK1δ-low tumors.
Supplementary Tables Table S1. TCGA RNA-seq and GISTIC2 copy number data and correlation analysis for breast cancer (BRCA) tumors. Case ID CSNK1D (log2 CNV) CSNK1D (log2 RNASeq) TCGA-B6-A1KF -1.043 10.3646 TCGA-OL-A5RZ -0.935 11.9216 TCGA-E2-A156-0.919 11.0154 TCGA-AR-A24S -0.902 10.1766 TCGA-D8-A1JN -0.876 11.6467 TCGA-D8-A13Y -0.831 10.7815 TCGA-EW-A1J1-0.828 11.5589 TCGA-D8-A1JA -0.815 10.3509 TCGA-D8-A1JM -0.79 10.9116 TCGA-A7-A0D9-0.773 11.2158 TCGA-AR-A0TY -0.749 10.8957 TCGA-B6-A0IG -0.737 11.3643 TCGA-E9-A1RF -0.737 11.0847 TCGA-GM-A2D9-0.728 11.2445 TCGA-C8-A1HL -0.696 10.7066 TCGA-A8-A07I -0.696 11.3485 TCGA-BH-A0DZ -0.677 10.8932 TCGA-A8-A09N -0.666 11.3283 TCGA-D8-A1XJ -0.658 11.0838 TCGA-D8-A1J8-0.65 10.6698 TCGA-AO-A0J5-0.647 11.2301 TCGA-PE-A5DD -0.645 11.5645 TCGA-C8-A12Z -0.639 11.4097 TCGA-D8-A27T -0.634 11.1288 TCGA-C8-A26W -0.619 11.0611 TCGA-D8-A27V -0.615 10.8951 TCGA-B6-A0IE -0.613 11.2025 TCGA-E2-A15H -0.599 11.3348 TCGA-AN-A0FW -0.598 11.4859 TCGA-D8-A1XU -0.59 11.3962 TCGA-BH-A0BC -0.585 11.1423 TCGA-B6-A0IK -0.583 11.3869 TCGA-A8-A08B -0.58 11.1066
TCGA-AQ-A54N -0.575 11.5861 TCGA-BH-A0EE -0.57 10.6764 TCGA-AN-A0FJ -0.564 10.8002 TCGA-BH-A18R -0.551 10.9778 TCGA-BH-A1EV -0.547 11.2127 TCGA-BH-A0B0-0.547 10.7963 TCGA-AC-A3W7-0.541 11.8549 TCGA-E2-A152-0.534 10.8425 TCGA-D8-A27R -0.517 10.5998 TCGA-A8-A094-0.511 10.7153 TCGA-BH-A1EN -0.51 11.0361 TCGA-D8-A1XZ -0.51 11.3353 TCGA-BH-A1EY -0.503 10.8349 TCGA-EW-A1PA -0.489 9.1674 TCGA-GM-A2DA -0.488 11.3281 TCGA-AO-A03V -0.488 11.3542 TCGA-A2-A4RW -0.486 11.7924 TCGA-AO-A0J3-0.485 11.729 TCGA-BH-A18F -0.479 11.0358 TCGA-AN-A0FD -0.479 11.6594 TCGA-E9-A1N6-0.473 11.3348 TCGA-AO-A0JD -0.467 11.2602 TCGA-AN-A04A -0.467 11.4649 TCGA-BH-A0HP -0.465 11.1104 TCGA-B6-A0RV -0.462 11.3354 TCGA-AO-A0JM -0.459 10.8099 TCGA-AR-A1AN -0.458 11.2867 TCGA-A7-A56D -0.456 11.4048 TCGA-AC-A3TM -0.445 11.5632 TCGA-BH-A18V -0.443 10.8238 TCGA-A8-A08G -0.441 11.554 TCGA-EW-A1OV -0.438 11.2837 TCGA-AC-A62Y -0.435 11.315 TCGA-AR-A250-0.432 11.1139 TCGA-AR-A0U3-0.431 10.7918 TCGA-AC-A3W5-0.427 11.5773 TCGA-E2-A14T -0.425 11.6371 TCGA-AN-A0AS -0.424 11.4479 TCGA-AR-A1AR -0.412 10.5239 TCGA-D8-A1Y1-0.409 11.4505
TCGA-E2-A14V -0.407 11.5734 TCGA-A8-A084-0.402 11.7266 TCGA-BH-A0BR -0.402 11.4581 TCGA-E2-A2P5-0.401 11.4643 TCGA-A7-A0CG -0.399 11.195 TCGA-BH-A0E0-0.399 10.9861 TCGA-C8-A138-0.398 11.3001 TCGA-AQ-A0Y5-0.395 11.227 TCGA-AR-A1AY -0.393 11.3138 TCGA-A1-A0SN -0.392 11.4434 TCGA-A2-A0D1-0.392 11.6464 TCGA-BH-A0C1-0.39 11.2753 TCGA-BH-A5J0-0.385 11.6825 TCGA-BH-A0B6-0.381 11.6639 TCGA-A2-A0CV -0.378 11.5556 TCGA-E9-A22A -0.376 10.7823 TCGA-E2-A150-0.362 11.0116 TCGA-A8-A0AD -0.361 11.2773 TCGA-BH-A0DP -0.361 11.3385 TCGA-BH-A1F6-0.358 11.0313 TCGA-OL-A5S0-0.354 11.5502 TCGA-C8-A3M7-0.351 11.2181 TCGA-B6-A0RU -0.341 11.0319 TCGA-C8-A132-0.338 11.6064 TCGA-BH-A18P -0.332 11.6283 TCGA-GI-A2C8-0.332 11.7843 TCGA-E9-A22G -0.331 11.1134 TCGA-AC-A3W6-0.329 11.7143 TCGA-E2-A1LL -0.325 11.3173 TCGA-E9-A22D -0.318 11.3161 TCGA-A2-A259-0.317 11.2675 TCGA-E2-A14X -0.315 10.9718 TCGA-AC-A2BM -0.312 11.1074 TCGA-A2-A0YK -0.307 11.2252 TCGA-E9-A1NH -0.299 11.6303 TCGA-B6-A0IB -0.297 11.8434 TCGA-A2-A0D0-0.293 11.0423 TCGA-A2-A25A -0.292 11.3016 TCGA-AO-A0JL -0.29 11.0765 TCGA-A1-A0SK -0.286 11.7043
TCGA-BH-A0BA -0.285 11.2389 TCGA-E2-A1B1-0.281 10.8264 TCGA-C8-A12P -0.28 11.0356 TCGA-PE-A5DE -0.273 11.532 TCGA-AO-A03N -0.272 11.1923 TCGA-A2-A1G1-0.263 11.1844 TCGA-C8-A26X -0.26 11.3289 TCGA-B6-A0IH -0.255 11.8344 TCGA-A2-A4RX -0.25 11.6541 TCGA-BH-A1EU -0.245 11.2847 TCGA-A7-A26F -0.245 11.012 TCGA-AN-A046-0.241 11.5057 TCGA-AR-A24R -0.24 11.4295 TCGA-A2-A3XZ -0.24 11.6166 TCGA-E2-A1II -0.239 10.8081 TCGA-BH-A208-0.237 11.1692 TCGA-BH-A0B5-0.234 11.531 TCGA-AO-A12D -0.226 11.6768 TCGA-AC-A3BB -0.225 11.8178 TCGA-E2-A14Z -0.223 11.4609 TCGA-D8-A145-0.213 11.7338 TCGA-A2-A0CR -0.211 11.798 TCGA-BH-A18I -0.207 11.6137 TCGA-A7-A26E -0.206 11.474 TCGA-C8-A131-0.203 11.2824 TCGA-A7-A26H -0.2 11.3063 TCGA-E2-A159-0.197 11.1713 TCGA-BH-A1FH -0.195 11.3169 TCGA-B6-A409-0.195 11.3477 TCGA-A7-A4SE -0.194 11.3592 TCGA-GM-A2DD -0.184 11.7375 TCGA-E9-A3X8-0.181 11.4156 TCGA-JL-A3YW -0.17 11.6582 TCGA-AC-A23H -0.167 11.4654 TCGA-A2-A3XY -0.165 11.6899 TCGA-A8-A08I -0.162 11.5608 TCGA-A2-A04U -0.16 10.7475 TCGA-BH-A18U -0.16 11.2564 TCGA-D8-A13Z -0.158 11.5019 TCGA-E2-A573-0.148 11.3517
TCGA-AR-A1AJ -0.145 10.7918 TCGA-GM-A2DI -0.142 11.5995 TCGA-A7-A4SD -0.142 11.761 TCGA-A2-A0SX -0.139 11.4065 TCGA-AN-A0FT -0.132 11.3057 TCGA-BH-A0E6-0.126 11.4112 TCGA-A8-A081-0.124 11.7432 TCGA-E2-A15G -0.122 11.8392 TCGA-A2-A04W -0.122 11.7519 TCGA-D8-A140-0.121 11.4791 TCGA-BH-A0RX -0.121 11.1444 TCGA-A2-A0EY -0.119 11.5472 TCGA-BH-A0E9-0.118 11.5636 TCGA-D8-A27N -0.112 11.5461 TCGA-E2-A15M -0.11 11.0259 TCGA-E2-A1B5-0.108 11.4169 TCGA-E9-A1NF -0.105 11.6209 TCGA-AR-A2LR -0.103 11.1628 TCGA-LL-A5YO -0.103 11.9804 TCGA-E2-A15E -0.097 11.7625 TCGA-AR-A24U -0.09 11.4234 TCGA-A8-A08L -0.089 11.8631 TCGA-EW-A2FR -0.086 11.5808 TCGA-A2-A0EP -0.085 11.6492 TCGA-D8-A1XW -0.08 10.755 TCGA-C8-A273-0.075 11.5462 TCGA-AR-A2LH -0.073 11.3952 TCGA-AQ-A04H -0.072 12.0864 TCGA-A2-A04X -0.07 11.4645 TCGA-E2-A14P -0.07 11.8421 TCGA-AN-A0XW -0.067 11.427 TCGA-E2-A108-0.064 11.3245 TCGA-E2-A1LI -0.063 11.0661 TCGA-AQ-A1H2-0.062 11.6527 TCGA-A8-A076-0.062 11.2264 TCGA-A2-A4S2-0.061 11.6498 TCGA-D8-A1JI -0.06 11.5829 TCGA-AO-A124-0.06 11.1313 TCGA-A1-A0SQ -0.059 10.9441 TCGA-BH-A28Q -0.058 11.5877
TCGA-D8-A1XR -0.056 11.7159 TCGA-AC-A23E -0.055 11.4752 TCGA-GM-A4E0-0.054 11.8001 TCGA-GM-A2DN -0.054 11.7757 TCGA-A7-A3IZ -0.053 12.128 TCGA-AR-A24N -0.052 11.2358 TCGA-E9-A2JT -0.05 11.7583 TCGA-A2-A0ER -0.05 11.3493 TCGA-E9-A1N4-0.049 11.0719 TCGA-B6-A0I1-0.047 12.0573 TCGA-E2-A1LG -0.047 10.9623 TCGA-A8-A0A7-0.046 11.5629 TCGA-E2-A10B -0.045 11.5127 TCGA-EW-A1P7-0.044 11.335 TCGA-AR-A5QM -0.043 11.6529 TCGA-D8-A27E -0.042 11.7528 TCGA-B6-A0RQ -0.042 11.8728 TCGA-A2-A0T2-0.042 11.0656 TCGA-A8-A09Q -0.042 11.3264 TCGA-AC-A5XS -0.04 12.0331 TCGA-BH-A0EA -0.038 11.8117 TCGA-A8-A09G -0.037 12.0441 TCGA-A2-A4RY -0.036 11.9822 TCGA-AR-A1AO -0.036 11.37 TCGA-E2-A15K -0.035 11.7037 TCGA-D8-A1XG -0.035 11.7851 TCGA-A2-A25C -0.034 11.3754 TCGA-EW-A2FS -0.034 11.5087 TCGA-E2-A14Q -0.034 11.7187 TCGA-E2-A1LE -0.033 11.724 TCGA-AO-A0JI -0.033 11.3763 TCGA-EW-A2FW -0.033 11.5708 TCGA-A2-A0CS -0.031 11.83 TCGA-AO-A1KO -0.031 11.1273 TCGA-BH-A0DX -0.031 11.0685 TCGA-AR-A2LQ -0.03 11.5189 TCGA-BH-A1FU -0.03 11.568 TCGA-A8-A07U -0.028 11.31 TCGA-BH-A0DL -0.028 11.3668 TCGA-D8-A1XO -0.027 11.498
TCGA-A8-A07S -0.026 11.6152 TCGA-E2-A14N -0.025 10.9886 TCGA-A7-A0CH -0.025 11.5348 TCGA-A2-A0ES -0.025 11.6 TCGA-BH-A0BJ -0.024 11.7699 TCGA-AO-A12A -0.023 11.5117 TCGA-AC-A2QI -0.022 12.3412 TCGA-A2-A25F -0.022 11.0767 TCGA-E9-A249-0.022 11.6221 TCGA-A2-A3Y0-0.021 11.8879 TCGA-A2-A0CQ -0.021 11.7208 TCGA-E2-A1IL -0.02 12.023 TCGA-B6-A0IA -0.02 11.1448 TCGA-E2-A1L9-0.02 11.1766 TCGA-GM-A5PX -0.02 11.7553 TCGA-BH-A0EI -0.02 11.6112 TCGA-AN-A0FS -0.02 11.8361 TCGA-A1-A0SI -0.019 11.309 TCGA-E9-A228-0.019 11.9831 TCGA-AN-A0XP -0.019 11.7936 TCGA-AR-A0TV -0.018 11.5417 TCGA-BH-A201-0.018 11.5462 TCGA-E2-A15P -0.018 11.8986 TCGA-D8-A1JS -0.018 11.4209 TCGA-BH-A0HI -0.018 11.6638 TCGA-AR-A2LJ -0.018 12.2476 TCGA-A8-A075-0.018 11.7351 TCGA-BH-A0DO -0.018 11.7144 TCGA-A2-A0EM -0.017 11.6584 TCGA-E9-A3Q9-0.017 11.5679 TCGA-E2-A15F -0.017 11.7296 TCGA-E2-A1BC -0.017 11.5242 TCGA-B6-A0WT -0.017 11.5238 TCGA-D8-A27G -0.016 11.8193 TCGA-BH-A0BD -0.016 11.5303 TCGA-AN-A0FX -0.016 11.6719 TCGA-AO-A128-0.015 11.2618 TCGA-A1-A0SF -0.015 11.8572 TCGA-D8-A1XC -0.015 11.6828 TCGA-A2-A3KD -0.015 11.6727
TCGA-AO-A12G -0.014 11.5954 TCGA-D8-A3Z6-0.013 11.7495 TCGA-AN-A0AT -0.013 11.4741 TCGA-BH-A0DQ -0.013 11.6116 TCGA-BH-A0H9-0.013 12.0772 TCGA-E2-A2P6-0.013 12.0295 TCGA-C8-A1HE -0.013 11.5783 TCGA-B6-A408-0.012 11.984 TCGA-E9-A1N5-0.012 11.7208 TCGA-BH-A42U -0.011 12.1446 TCGA-A7-A3J1-0.011 12.1132 TCGA-AN-A03Y -0.011 11.9633 TCGA-LL-A5YL -0.011 11.9838 TCGA-A8-A09V -0.011 11.7336 TCGA-AR-A24M -0.011 11.1732 TCGA-AR-A5QQ -0.01 11.6622 TCGA-E9-A1R0-0.01 12.0081 TCGA-A2-A0YI -0.01 11.818 TCGA-B6-A0X5-0.01 11.0321 TCGA-OL-A5RU -0.01 12.0282 TCGA-A8-A0A1-0.009 11.5289 TCGA-AR-A24W -0.009 11.5911 TCGA-A1-A0SE -0.008 11.6774 TCGA-BH-A42V -0.008 11.9657 TCGA-E2-A15I -0.008 11.975 TCGA-A7-A3IY -0.008 11.8274 TCGA-A2-A3KC -0.007 11.7434 TCGA-BH-A0BM -0.007 11.2484 TCGA-AR-A1AL -0.007 11.6067 TCGA-AC-A23C -0.007 11.099 TCGA-BH-A0BQ -0.007 11.6318 TCGA-EW-A1PB -0.006 11.5289 TCGA-E9-A1RD -0.006 11.4992 TCGA-A8-A0A4-0.006 11.5275 TCGA-A2-A3XW -0.005 12.0606 TCGA-B6-A0RO -0.005 10.8708 TCGA-AN-A0FF -0.005 11.7241 TCGA-A7-A13G -0.005 11.8121 TCGA-D8-A1JU -0.004 11.5369 TCGA-GM-A2DM -0.004 11.9069
TCGA-BH-A18K -0.004 11.4408 TCGA-D8-A1XD -0.004 11.9255 TCGA-AR-A0TR -0.004 11.8997 TCGA-B6-A0IC -0.004 11.9687 TCGA-D8-A27L -0.004 11.883 TCGA-AR-A24T -0.004 11.5315 TCGA-C8-A275-0.004 11.4063 TCGA-E2-A570-0.004 12.0158 TCGA-A2-A4S0-0.003 11.8958 TCGA-AC-A2FG -0.003 11.8846 TCGA-A2-A3XS -0.003 11.9428 TCGA-EW-A1P0-0.003 11.4961 TCGA-A2-A0D3-0.003 11.7123 TCGA-C8-A133-0.003 11.7409 TCGA-B6-A0I5-0.003 11.557 TCGA-B6-A0X0-0.003 11.8499 TCGA-E2-A155-0.003 11.8366 TCGA-B6-A0RT -0.002 11.9426 TCGA-B6-A0X4-0.002 11.7033 TCGA-OL-A5RV -0.002 12.2458 TCGA-E9-A245-0.002 12.0704 TCGA-AO-A0J8-0.002 11.9023 TCGA-A8-A095-0.002 11.239 TCGA-D8-A1XA -0.002 12.0245 TCGA-A7-A5ZW -0.002 11.8164 TCGA-A7-A425-0.002 12.3298 TCGA-D8-A27K -0.002 11.6865 TCGA-B6-A0IP -0.002 12.1183 TCGA-EW-A1J3-0.002 11.1423 TCGA-C8-A12T -0.001 11.8839 TCGA-BH-A0DV -0.001 11.4264 TCGA-A8-A096-0.001 11.4639 TCGA-A1-A0SB -0.001 11.6598 TCGA-BH-A0H3-0.001 11.6893 TCGA-C8-A12Y -0.001 11.4211 TCGA-BH-A28O -0.001 11.9644 TCGA-E2-A1IK -0.001 11.8084 TCGA-AO-A0JF -0.001 11.5047 TCGA-A2-A1G6-0.001 11.4601 TCGA-AO-A12H -0.001 11.9181
TCGA-A2-A0YD 0 11.6167 TCGA-BH-A0DS 0 11.4654 TCGA-AN-A0XV 0 11.4873 TCGA-BH-A0BO 0 12.2957 TCGA-AQ-A04L 0 11.6593 TCGA-EW-A1P8 0 11.5048 TCGA-B6-A40B 0 12.3944 TCGA-OL-A5RW 0 11.378 TCGA-AC-A3YJ 0 12.1438 TCGA-BH-A0GZ 0 11.8576 TCGA-BH-A1FL 0 12.0912 TCGA-BH-A1FR 0 11.9702 TCGA-E9-A1RC 0 11.7807 TCGA-A8-A083 0 11.6224 TCGA-AR-A0TW 0.001 12.0947 TCGA-OL-A5RX 0.001 12.0143 TCGA-A2-A0T5 0.001 11.5058 TCGA-B6-A0WS 0.001 11.4545 TCGA-EW-A1IX 0.001 11.874 TCGA-AC-A3YI 0.001 12.3767 TCGA-D8-A1JH 0.002 11.6454 TCGA-GM-A3XG 0.002 12.027 TCGA-EW-A1PE 0.002 11.4538 TCGA-OL-A5RY 0.002 11.7571 TCGA-A7-A13E 0.002 11.055 TCGA-AR-A24O 0.002 11.4428 TCGA-C8-A274 0.002 11.7021 TCGA-BH-A0B7 0.002 11.9312 TCGA-AN-A0FK 0.003 11.6233 TCGA-D8-A1XV 0.003 11.4035 TCGA-BH-A0H5 0.003 11.8281 TCGA-EW-A1IY 0.003 10.7069 TCGA-GM-A2DB 0.003 11.7265 TCGA-B6-A0WZ 0.003 11.41 TCGA-D8-A27P 0.003 11.8028 TCGA-A7-A3RF 0.003 12.0869 TCGA-A8-A091 0.004 12.0792 TCGA-AC-A3OD 0.004 11.9735 TCGA-BH-A1FB 0.004 11.6132 TCGA-A2-A1FZ 0.004 11.4407
TCGA-E2-A15R 0.004 11.6117 TCGA-AR-A1AM 0.005 12.4394 TCGA-E2-A1IO 0.005 11.9329 TCGA-AO-A125 0.005 11.4683 TCGA-BH-A0HK 0.005 11.2696 TCGA-D8-A4Z1 0.005 12.1648 TCGA-EW-A2FV 0.005 11.4251 TCGA-AO-A126 0.005 11.873 TCGA-E9-A1NG 0.005 11.2439 TCGA-AR-A256 0.005 11.2195 TCGA-A2-A0EW 0.005 11.7735 TCGA-E2-A1L8 0.006 11.6199 TCGA-D8-A27I 0.006 11.7076 TCGA-E2-A1L6 0.006 11.551 TCGA-OK-A5Q2 0.006 11.8559 TCGA-A2-A0ST 0.006 11.6197 TCGA-AN-A0FN 0.006 11.3007 TCGA-BH-A0E1 0.006 11.2788 TCGA-BH-A0W3 0.006 12.0944 TCGA-OL-A66J 0.006 12.0801 TCGA-AC-A2B8 0.006 11.5121 TCGA-AR-A1AU 0.006 11.7411 TCGA-AR-A2LO 0.006 12.0262 TCGA-D8-A3Z5 0.006 12.2144 TCGA-LL-A442 0.007 12.3858 TCGA-OL-A66I 0.007 11.3716 TCGA-A2-A0YJ 0.007 10.8807 TCGA-BH-A1F8 0.007 11.3223 TCGA-D8-A141 0.007 11.504 TCGA-BH-A0HO 0.007 11.3596 TCGA-E2-A15J 0.007 11.7208 TCGA-A8-A08Z 0.007 11.605 TCGA-AC-A2FF 0.007 11.5213 TCGA-BH-A0BS 0.007 11.4787 TCGA-AR-A2LM 0.008 11.6969 TCGA-BH-A0EB 0.008 11.7497 TCGA-AO-A03U 0.008 11.4718 TCGA-E9-A227 0.008 11.4565 TCGA-E2-A14U 0.008 12.2864 TCGA-GM-A5PV 0.009 12.0014
TCGA-A7-A0DB 0.009 11.8564 TCGA-D8-A1X8 0.009 11.6167 TCGA-A8-A09Z 0.009 12.0627 TCGA-A2-A0T4 0.01 11.664 TCGA-EW-A1IW 0.01 11.1387 TCGA-BH-A0W4 0.01 11.8021 TCGA-A2-A0EO 0.01 11.9303 TCGA-OL-A66H 0.011 12.0353 TCGA-A2-A0YG 0.011 11.7047 TCGA-E9-A229 0.011 11.6461 TCGA-A8-A082 0.011 11.3999 TCGA-AC-A2FE 0.011 11.9883 TCGA-E9-A1N3 0.012 11.8685 TCGA-AC-A3QP 0.012 11.9534 TCGA-GM-A3XN 0.012 12.0816 TCGA-AR-A0TT 0.012 11.7247 TCGA-BH-A0DT 0.012 11.5833 TCGA-A8-A07J 0.012 11.7786 TCGA-BH-A0DH 0.012 10.9333 TCGA-A2-A0YL 0.012 11.4918 TCGA-E2-A1LH 0.013 11.4122 TCGA-E9-A22H 0.013 11.4801 TCGA-AO-A03M 0.013 12.0547 TCGA-E2-A1IF 0.013 11.8029 TCGA-HN-A2OB 0.013 11.9466 TCGA-AO-A0JC 0.013 11.4188 TCGA-E2-A1IU 0.013 11.7282 TCGA-BH-A2L8 0.014 12.0419 TCGA-BH-A0W5 0.014 11.8119 TCGA-E9-A24A 0.014 11.4805 TCGA-A7-A13H 0.014 12.3795 TCGA-LL-A50Y 0.015 12.0832 TCGA-E2-A10E 0.015 11.6855 TCGA-E9-A5FK 0.015 12.091 TCGA-A8-A07F 0.015 11.2929 TCGA-E2-A154 0.015 11.7525 TCGA-BH-A0GY 0.015 11.8592 TCGA-BH-A1ET 0.015 11.3871 TCGA-OL-A5DA 0.016 12.1411 TCGA-AR-A2LE 0.016 11.6937
TCGA-B6-A0X7 0.016 11.9233 TCGA-AC-A2FB 0.017 11.7491 TCGA-AC-A2FK 0.017 11.7 TCGA-A8-A0A6 0.017 11.4946 TCGA-BH-A1FE 0.017 11.3544 TCGA-AC-A3TN 0.017 12.316 TCGA-EW-A1PF 0.017 11.8798 TCGA-E2-A10A 0.018 11.7739 TCGA-OL-A5D6 0.018 12.4341 TCGA-B6-A0RP 0.018 11.8483 TCGA-E2-A1B4 0.018 11.7839 TCGA-A2-A1G4 0.018 11.5959 TCGA-AR-A2LN 0.018 11.6262 TCGA-EW-A3E8 0.019 11.9242 TCGA-A8-A06T 0.019 11.7723 TCGA-AR-A24X 0.019 11.4684 TCGA-A7-A5ZX 0.019 11.9544 TCGA-AN-A03X 0.019 11.1609 TCGA-A2-A0SY 0.019 11.7836 TCGA-A8-A06Y 0.019 11.954 TCGA-C8-A12N 0.02 11.5285 TCGA-BH-A0B9 0.02 11.9673 TCGA-C8-A12X 0.021 11.7146 TCGA-A8-A09T 0.021 11.749 TCGA-AR-A0TZ 0.021 12.2622 TCGA-AR-A1AS 0.022 11.8881 TCGA-AC-A3HN 0.022 11.7812 TCGA-A8-A08C 0.022 11.4914 TCGA-A2-A0CP 0.022 11.8325 TCGA-A2-A0T6 0.022 11.7512 TCGA-E9-A1R3 0.023 11.6008 TCGA-AO-A1KT 0.023 11.8109 TCGA-BH-A0E7 0.023 11.7744 TCGA-E9-A54X 0.023 12.158 TCGA-GM-A3NY 0.023 11.8117 TCGA-A1-A0SG 0.023 11.8033 TCGA-AC-A5EH 0.023 12.2857 TCGA-AR-A254 0.024 11.3669 TCGA-A8-A099 0.024 10.9765 TCGA-GM-A3NW 0.024 12.2132
TCGA-OL-A5D8 0.024 11.7967 TCGA-AR-A5QP 0.025 12.0188 TCGA-AO-A0JA 0.025 11.6373 TCGA-B6-A40C 0.025 12.2979 TCGA-E9-A1N8 0.025 11.9359 TCGA-BH-A0H0 0.027 11.9187 TCGA-E2-A15O 0.027 11.4193 TCGA-AN-A0XN 0.027 11.2716 TCGA-D8-A1X6 0.028 11.4427 TCGA-AO-A03R 0.028 11.4706 TCGA-E9-A3HO 0.028 11.5028 TCGA-BH-A1EO 0.028 11.3096 TCGA-E2-A10F 0.028 11.7295 TCGA-A8-A08H 0.029 11.3465 TCGA-AQ-A04J 0.029 11.4846 TCGA-BH-A0HA 0.029 11.5576 TCGA-JL-A3YX 0.03 12.3383 TCGA-GM-A2DL 0.03 11.7032 TCGA-LL-A440 0.031 12.0971 TCGA-E2-A3DX 0.031 11.8311 TCGA-E2-A15C 0.032 11.6502 TCGA-A2-A04Q 0.032 11.7329 TCGA-BH-A1F5 0.032 11.0591 TCGA-BH-A18M 0.032 11.5624 TCGA-AC-A3EH 0.032 12.4623 TCGA-C8-A12K 0.032 11.295 TCGA-AC-A2FO 0.033 11.9667 TCGA-A2-A0EX 0.033 11.8756 TCGA-A2-A1FV 0.033 11.3886 TCGA-BH-A0AU 0.033 11.7852 TCGA-E2-A1IN 0.034 11.6105 TCGA-AR-A5QN 0.034 12.0952 TCGA-E9-A1ND 0.034 11.6336 TCGA-E9-A1N9 0.034 11.577 TCGA-A8-A0A9 0.034 12.2678 TCGA-B6-A0RM 0.035 11.7559 TCGA-AR-A0U0 0.036 11.1544 TCGA-BH-A0HB 0.036 11.7975 TCGA-B6-A0RN 0.037 11.9463 TCGA-E2-A1BD 0.038 11.919
TCGA-B6-A0IM 0.039 12.037 TCGA-AR-A1AX 0.039 12.0703 TCGA-A2-A04V 0.039 11.9389 TCGA-E2-A15D 0.04 11.6808 TCGA-BH-A0H6 0.04 11.6481 TCGA-C8-A26V 0.041 11.5202 TCGA-AO-A0J9 0.041 11.352 TCGA-B6-A0IJ 0.043 11.5088 TCGA-BH-A1FD 0.043 11.2156 TCGA-A8-A07E 0.043 11.8442 TCGA-A8-A09I 0.044 11.538 TCGA-EW-A1P6 0.044 11.8057 TCGA-A8-A0A2 0.045 12.3132 TCGA-A2-A0YF 0.045 11.3061 TCGA-C8-A134 0.046 11.3199 TCGA-BH-A0W7 0.046 11.7465 TCGA-GM-A2DF 0.047 11.7215 TCGA-E2-A14S 0.048 11.5593 TCGA-D8-A1JP 0.048 12.0107 TCGA-A7-A26I 0.049 10.801 TCGA-C8-A1HJ 0.05 10.9349 TCGA-E2-A15L 0.051 11.4228 TCGA-AN-A0XS 0.051 11.7236 TCGA-A8-A08T 0.051 11.9645 TCGA-E2-A1B6 0.052 11.0914 TCGA-AN-A0AL 0.053 11.5864 TCGA-A8-A06X 0.054 11.7714 TCGA-E9-A248 0.055 11.389 TCGA-A2-A0EN 0.056 11.4707 TCGA-PE-A5DC 0.057 12.1225 TCGA-D8-A146 0.057 11.7943 TCGA-AR-A0TP 0.057 11.1947 TCGA-AN-A0AK 0.058 11.5323 TCGA-A8-A06P 0.059 11.7336 TCGA-D8-A1Y0 0.061 11.6102 TCGA-A8-A09C 0.061 11.9607 TCGA-E2-A1LB 0.062 12.1172 TCGA-A2-A0T7 0.063 12.0586 TCGA-LQ-A4E4 0.063 12.3877 TCGA-AR-A1AH 0.064 11.7315
TCGA-BH-A0BT 0.064 11.8034 TCGA-A8-A08X 0.065 11.38 TCGA-BH-A42T 0.065 12.4912 TCGA-A2-A0CO 0.065 12.2531 TCGA-BH-A18J 0.066 12.1309 TCGA-AO-A12F 0.067 11.4088 TCGA-B6-A0WW 0.068 11.7969 TCGA-AO-A0JE 0.07 11.4986 TCGA-B6-A0WX 0.071 11.5309 TCGA-BH-A0BV 0.071 11.2827 TCGA-GM-A2DH 0.071 11.5981 TCGA-AR-A1AP 0.071 12.0529 TCGA-B6-A0RL 0.072 12.3331 TCGA-A1-A0SD 0.075 11.8468 TCGA-D8-A1Y3 0.077 11.601 TCGA-B6-A0RH 0.079 11.8495 TCGA-AO-A1KP 0.08 11.0919 TCGA-A2-A0CK 0.08 12.2024 TCGA-AN-A0XR 0.08 11.9487 TCGA-BH-A0DK 0.081 11.5953 TCGA-A7-A0DA 0.081 11.6348 TCGA-A7-A4SF 0.082 12.2756 TCGA-AR-A1AQ 0.084 11.5074 TCGA-E9-A1RB 0.085 11.5857 TCGA-A7-A426 0.088 12.0283 TCGA-D8-A1JJ 0.089 11.6722 TCGA-AR-A0U1 0.089 11.5947 TCGA-A2-A0SV 0.089 11.5248 TCGA-EW-A424 0.092 12.1491 TCGA-A2-A0YH 0.093 11.7122 TCGA-D8-A1JE 0.096 11.183 TCGA-A2-A3XX 0.097 11.4719 TCGA-D8-A1JD 0.098 11.5513 TCGA-A2-A04N 0.098 11.6571 TCGA-D8-A1XB 0.098 11.8415 TCGA-AR-A0U2 0.101 11.9113 TCGA-C8-A1HI 0.101 11.8777 TCGA-E9-A226 0.102 11.3016 TCGA-A7-A0CE 0.102 11.6286 TCGA-AN-A0XO 0.104 11.8075
TCGA-BH-A0HU 0.104 12.0177 TCGA-E2-A158 0.106 11.65 TCGA-BH-A204 0.107 11.2062 TCGA-D8-A1JG 0.109 11.7821 TCGA-B6-A1KI 0.113 11.9319 TCGA-LL-A441 0.117 11.9382 TCGA-B6-A0IQ 0.117 11.77 TCGA-B6-A3ZX 0.12 12.0377 TCGA-A2-A0CW 0.12 11.6111 TCGA-E2-A1B0 0.122 11.3319 TCGA-EW-A1OW 0.123 11.3132 TCGA-AR-A0TS 0.127 11.4598 TCGA-BH-A0AV 0.127 11.7347 TCGA-E9-A22E 0.128 11.2361 TCGA-A2-A3XU 0.131 11.6745 TCGA-GM-A2DO 0.132 12.1545 TCGA-C8-A27A 0.132 11.7267 TCGA-EW-A1PG 0.133 11.6156 TCGA-A2-A1FX 0.142 11.8707 TCGA-D8-A1JC 0.142 11.9354 TCGA-AR-A1AI 0.142 11.5158 TCGA-D8-A1JK 0.143 11.5229 TCGA-E9-A1R4 0.147 11.552 TCGA-BH-A0BL 0.149 11.1747 TCGA-A8-A08P 0.149 11.5914 TCGA-E2-A14Y 0.151 11.1147 TCGA-BH-A209 0.155 11.1749 TCGA-C8-A130 0.16 11.7766 TCGA-AC-A3QQ 0.161 12.1509 TCGA-E2-A10C 0.161 12.0656 TCGA-D8-A1JF 0.163 11.6537 TCGA-A2-A0D4 0.164 12.2705 TCGA-MS-A51U 0.165 11.8158 TCGA-D8-A1XQ 0.169 11.4941 TCGA-A2-A0CL 0.173 11.8318 TCGA-AR-A1AW 0.173 11.4407 TCGA-E2-A1LK 0.177 11.3758 TCGA-E9-A1NA 0.178 11.8397 TCGA-BH-A1FJ 0.181 11.5569 TCGA-AC-A23G 0.182 11.7997
TCGA-AC-A2QJ 0.182 12.2025 TCGA-BH-A1FN 0.187 11.2529 TCGA-A8-A08S 0.187 12.2145 TCGA-AR-A1AV 0.197 12.0618 TCGA-A2-A0CM 0.197 11.5333 TCGA-AO-A1KS 0.201 11.167 TCGA-BH-A0WA 0.201 11.5568 TCGA-AO-A129 0.202 11.7548 TCGA-E2-A15A 0.203 11.5169 TCGA-B6-A0WY 0.203 11.7514 TCGA-BH-A0H7 0.204 12.0229 TCGA-C8-A1HO 0.207 11.4962 TCGA-B6-A401 0.213 12.0871 TCGA-E2-A1IH 0.214 11.1413 TCGA-D8-A27M 0.216 11.624 TCGA-A7-A4SA 0.217 12.7132 TCGA-A8-A09X 0.227 11.3593 TCGA-A2-A0D2 0.232 11.7835 TCGA-A8-A09B 0.235 11.9892 TCGA-OL-A66K 0.236 12.2134 TCGA-BH-A1FM 0.237 10.7257 TCGA-AO-A0J4 0.237 11.3526 TCGA-E2-A1AZ 0.239 11.0279 TCGA-BH-A18H 0.251 12.2757 TCGA-BH-A1F0 0.252 11.3959 TCGA-A2-A0CU 0.253 12.5664 TCGA-BH-A0BZ 0.255 12.1026 TCGA-C8-A12O 0.256 11.5193 TCGA-C8-A12Q 0.26 11.7751 TCGA-A1-A0SP 0.261 11.9585 TCGA-AO-A0JJ 0.263 11.3904 TCGA-E2-A107 0.265 12.3499 TCGA-E9-A1RH 0.267 11.3578 TCGA-D8-A1JB 0.273 12.0889 TCGA-GM-A3XL 0.274 11.8974 TCGA-BH-A0E2 0.274 11.735 TCGA-EW-A1J2 0.28 11.8249 TCGA-C8-A26Y 0.285 12.045 TCGA-A8-A0AB 0.295 12.3079 TCGA-B6-A402 0.296 11.7134
TCGA-AR-A255 0.301 11.5101 TCGA-BH-A202 0.304 11.4254 TCGA-B6-A0RS 0.306 11.5568 TCGA-C8-A1HG 0.306 11.3745 TCGA-BH-A0DI 0.311 11.9028 TCGA-E9-A295 0.311 11.8997 TCGA-A8-A06Q 0.314 12.1844 TCGA-AN-A041 0.314 11.9889 TCGA-A2-A0EU 0.315 11.9075 TCGA-E2-A153 0.316 11.6559 TCGA-A8-A09K 0.316 12.2107 TCGA-E2-A1IJ 0.317 11.9508 TCGA-E2-A574 0.322 11.754 TCGA-AO-A0J7 0.326 12.5702 TCGA-A8-A08O 0.326 11.9419 TCGA-AN-A0FY 0.331 12.0805 TCGA-GM-A2DK 0.332 12.0038 TCGA-E9-A1QZ 0.334 11.8676 TCGA-A8-A07B 0.334 11.9846 TCGA-EW-A1J6 0.334 11.537 TCGA-C8-A1HM 0.336 11.6639 TCGA-E9-A243 0.337 11.388 TCGA-C8-A12V 0.339 12.0051 TCGA-BH-A0HQ 0.348 12.0618 TCGA-A8-A07G 0.349 12.0275 TCGA-EW-A3U0 0.35 11.7726 TCGA-AC-A5XU 0.35 12.3579 TCGA-BH-A1ES 0.352 11.6413 TCGA-A8-A090 0.359 11.7658 TCGA-A2-A0CX 0.363 11.7279 TCGA-AR-A24K 0.368 11.8685 TCGA-A2-A0YT 0.372 11.7833 TCGA-EW-A1PH 0.372 11.3175 TCGA-BH-A1EX 0.372 11.7389 TCGA-BH-A0AY 0.373 11.7405 TCGA-A7-A4SB 0.377 12.611 TCGA-E9-A247 0.379 11.9739 TCGA-EW-A1P3 0.379 11.7391 TCGA-E9-A1NE 0.38 11.839 TCGA-D8-A142 0.381 11.3717
TCGA-EW-A423 0.384 12.6555 TCGA-AQ-A1H3 0.393 11.8298 TCGA-C8-A27B 0.4 11.3114 TCGA-B6-A0I9 0.401 12.4076 TCGA-AO-A03P 0.402 12.0211 TCGA-C8-A12W 0.404 11.731 TCGA-LL-A5YN 0.407 12.525 TCGA-AN-A0XL 0.407 11.7592 TCGA-EW-A1P5 0.409 11.8761 TCGA-BH-A18T 0.414 11.6526 TCGA-AN-A0FV 0.415 12.2618 TCGA-D8-A1Y2 0.424 12.0278 TCGA-AR-A2LK 0.424 12.2885 TCGA-D8-A1XF 0.427 12.1605 TCGA-E9-A3QA 0.429 12.514 TCGA-AO-A12E 0.429 11.8299 TCGA-AR-A0U4 0.431 11.9696 TCGA-AR-A24Z 0.439 11.6432 TCGA-BH-A0AZ 0.441 11.7854 TCGA-D8-A1XM 0.445 12.0435 TCGA-B6-A0IO 0.445 12.5804 TCGA-BH-A0DE 0.446 12.1908 TCGA-E2-A14O 0.448 12.03 TCGA-E9-A5FL 0.45 12.2091 TCGA-C8-A1HK 0.451 12.0391 TCGA-AN-A0AJ 0.451 12.0052 TCGA-D8-A1J9 0.454 12.0566 TCGA-A8-A08R 0.455 11.623 TCGA-AO-A12B 0.456 11.3925 TCGA-E9-A1R6 0.459 12.2855 TCGA-E9-A244 0.46 11.3525 TCGA-A2-A0ET 0.464 12.4481 TCGA-A1-A0SH 0.465 11.6785 TCGA-BH-A0BF 0.465 11.8742 TCGA-BH-A0DD 0.467 11.8489 TCGA-A2-A0EQ 0.472 12.0048 TCGA-AR-A252 0.473 11.4807 TCGA-BH-A0C3 0.474 11.4914 TCGA-EW-A1J5 0.474 11.9125 TCGA-A8-A07O 0.477 11.6157
TCGA-AR-A0TX 0.485 12.3589 TCGA-A8-A06Z 0.488 12.2099 TCGA-GI-A2C9 0.493 11.6459 TCGA-C8-A26Z 0.494 12.1038 TCGA-AO-A0JG 0.504 12.5822 TCGA-E2-A56Z 0.506 12.2462 TCGA-A2-A1G0 0.508 11.821 TCGA-BH-A1EW 0.508 12.0536 TCGA-BH-A18N 0.511 12.0196 TCGA-OL-A5D7 0.513 12.4929 TCGA-A8-A093 0.519 11.8747 TCGA-A2-A0SU 0.521 12.5653 TCGA-BH-A0BP 0.524 12.2384 TCGA-B6-A0IN 0.524 11.7796 TCGA-D8-A1XT 0.527 11.9042 TCGA-E9-A1R2 0.529 12.059 TCGA-A2-A25D 0.531 12.1032 TCGA-AR-A24V 0.531 11.7285 TCGA-E9-A1R7 0.54 11.8832 TCGA-D8-A143 0.546 11.7215 TCGA-A2-A04Y 0.548 11.826 TCGA-AR-A24P 0.55 12.0684 TCGA-A7-A26J 0.55 11.8227 TCGA-E9-A1R5 0.552 11.9587 TCGA-A1-A0SJ 0.556 11.7911 TCGA-E2-A1L7 0.56 12.1481 TCGA-C8-A3M8 0.56 12.1371 TCGA-AO-A03T 0.564 11.9011 TCGA-E9-A1RE 0.564 11.726 TCGA-BH-A0C7 0.565 11.8591 TCGA-A8-A06O 0.566 12.1074 TCGA-AC-A2QH 0.569 11.7652 TCGA-D8-A27F 0.577 11.5589 TCGA-C8-A12L 0.577 11.7014 TCGA-AN-A0FZ 0.577 12.1569 TCGA-BH-A0BW 0.581 11.6911 TCGA-A2-A3XV 0.584 12.3017 TCGA-AR-A24H 0.587 11.5018 TCGA-B6-A2IU 0.588 12.3094 TCGA-A2-A0YC 0.591 11.9595
TCGA-B6-A0RE 0.591 12.1321 TCGA-A7-A26G 0.594 11.4793 TCGA-GM-A2DC 0.598 12.4771 TCGA-AR-A0TQ 0.602 12.2273 TCGA-C8-A1HF 0.606 11.7195 TCGA-A2-A25E 0.613 11.7823 TCGA-A8-A07P 0.619 11.7331 TCGA-D8-A27W 0.62 11.7622 TCGA-B6-A1KN 0.624 12.0373 TCGA-D8-A1X7 0.629 11.7416 TCGA-E2-A1IE 0.63 12.1541 TCGA-BH-A1FC 0.637 11.8414 TCGA-D8-A27H 0.65 11.8682 TCGA-AO-A0J6 0.653 11.4469 TCGA-AC-A62X 0.656 12.1512 TCGA-A2-A3XT 0.656 12.1477 TCGA-B6-A400 0.662 12.0736 TCGA-BH-A5IZ 0.672 12.5899 TCGA-B6-A0WV 0.679 12.0198 TCGA-BH-A0BG 0.679 11.8266 TCGA-AO-A03L 0.681 12.1049 TCGA-A2-A25B 0.693 11.7272 TCGA-AR-A251 0.698 11.8978 TCGA-AN-A049 0.705 12.0903 TCGA-B6-A0X1 0.706 11.9575 TCGA-A2-A0SW 0.709 11.8997 TCGA-AN-A0FL 0.712 11.9925 TCGA-A7-A3J0 0.713 12.1581 TCGA-AO-A03O 0.715 12.3445 TCGA-BH-A18S 0.716 11.7406 TCGA-A8-A07L 0.717 12.3152 TCGA-E2-A14R 0.72 11.2475 TCGA-B6-A1KC 0.721 11.9495 TCGA-D8-A1JL 0.727 12.1361 TCGA-E9-A1RI 0.73 11.8358 TCGA-A8-A086 0.731 11.7311 TCGA-C8-A1HN 0.732 12.1627 TCGA-BH-A1F2 0.732 11.279 TCGA-A2-A0YM 0.733 11.4883 TCGA-AR-A24Q 0.734 11.4677
TCGA-AQ-A54O 0.74 12.359 TCGA-A8-A07R 0.741 12.4764 TCGA-A8-A06U 0.742 12.2267 TCGA-A1-A0SO 0.744 11.3751 TCGA-A7-A13F 0.751 11.3486 TCGA-BH-A0B3 0.756 11.9527 TCGA-D8-A1XY 0.759 11.7629 TCGA-AN-A0XT 0.76 12.472 TCGA-AR-A1AK 0.76 12.0525 TCGA-E9-A22B 0.774 12.1239 TCGA-AN-A04D 0.779 11.8129 TCGA-A2-A0CT 0.781 11.8973 TCGA-LL-A5YM 0.799 12.1818 TCGA-BH-A0HX 0.803 12.2007 TCGA-E2-A15T 0.814 12.19 TCGA-D8-A1JT 0.817 11.1395 TCGA-AR-A24L 0.818 12.065 TCGA-B6-A0RI 0.829 11.9885 TCGA-B6-A0I2 0.83 12.1782 TCGA-A8-A097 0.832 12.2237 TCGA-E2-A15S 0.844 12.4155 TCGA-A8-A07W 0.847 12.1719 TCGA-BH-A203 0.852 12.2729 TCGA-E9-A5UO 0.855 12.2877 TCGA-AN-A0AM 0.865 12.8011 TCGA-BH-A1FG 0.866 11.9756 TCGA-D8-A1XL 0.873 11.9784 TCGA-A2-A1FW 0.879 12.2696 TCGA-HN-A2NL 0.884 12.2139 TCGA-AC-A2FM 0.888 12.7313 TCGA-A2-A0EV 0.894 12.4632 TCGA-E9-A1NI 0.913 11.9332 TCGA-AN-A0XU 0.916 12.3559 TCGA-AO-A0J2 0.934 12.3364 TCGA-A8-A09D 0.939 12.4809 TCGA-A2-A04T 0.941 12.0598 TCGA-B6-A0RG 0.943 11.6877 TCGA-A8-A092 0.947 12.0607 TCGA-BH-A18Q 0.947 11.7939 TCGA-C8-A12U 0.952 12.0746
TCGA-AO-A1KR 0.953 12.6042 TCGA-A8-A06R 0.977 11.9482 TCGA-A7-A0CJ 0.979 11.9592 TCGA-D8-A1XS 0.984 12.0443 TCGA-AC-A2BK 0.985 12.6516 TCGA-AN-A04C 0.992 12.3203 TCGA-BH-A0DG 0.994 12.3982 TCGA-A8-A09A 1.003 11.8316 TCGA-D8-A1XK 1.006 12.7212 TCGA-A8-A06N 1.041 12.6143 TCGA-A8-A09R 1.043 12.4595 TCGA-D8-A147 1.054 11.7882 TCGA-EW-A1PC 1.065 12.4379 TCGA-EW-A1P4 1.074 12.3612 TCGA-A7-A13D 1.082 11.998 TCGA-A1-A0SM 1.09 12.2759 TCGA-A2-A4S3 1.103 12.7856 TCGA-A8-A09M 1.11 12.3791 TCGA-BH-A18L 1.121 12.4959 TCGA-C8-A135 1.126 12.4547 TCGA-D8-A1X5 1.127 12.0839 TCGA-BH-A0HY 1.147 12.5744 TCGA-A2-A04P 1.182 11.8883 TCGA-EW-A1OY 1.183 12.284 TCGA-LL-A5YP 1.241 12.3568 TCGA-E2-A105 1.271 12.7615 TCGA-D8-A1X9 1.278 12.156 TCGA-EW-A1PD 1.283 12.4011 TCGA-A2-A0T0 1.287 12.2354 TCGA-AR-A2LL 1.324 12.6424 TCGA-C8-A137 1.366 12.3692 TCGA-E2-A1IG 1.374 12.3759 TCGA-BH-A0AW 1.407 11.8353 TCGA-BH-A0C0 1.431 12.5057 TCGA-A8-A085 1.434 12.7405 TCGA-A7-A0CD 1.437 12.4127 TCGA-BH-A0HW 1.496 12.6943 TCGA-A2-A04R 1.524 12.5981 TCGA-A8-A08F 1.538 12.5197 TCGA-E2-A1LA 1.552 12.262
TCGA-BH-A18G 1.609 12.286 TCGA-E9-A2JS 1.614 12.5011 TCGA-BH-A0B4 1.626 12.4567 TCGA-A7-A5ZV 1.649 12.0362 TCGA-AO-A1KQ 1.663 12.3032 TCGA-A8-A09W 1.802 11.7836 TCGA-A8-A079 1.822 12.7233 TCGA-EW-A1OZ 1.826 12.9265 TCGA-A7-A2KD 1.837 12.5368 TCGA-A2-A0T3 1.86 12.3457 TCGA-C8-A278 2.125 13.3421 TCGA-E2-A109 2.126 12.7038 TCGA-A2-A0YE 2.131 13.3441 TCGA-E2-A14W 2.215 12.6306 TCGA-C8-A12M 2.253 13.2875 TCGA-E9-A5UP 2.427 13.113 TCGA-A2-A0T1 2.5 13.1671 TCGA-A8-A08J 3.657 13.3911 TCGA-EW-A1OX 3.657 13.2868 Parameter Pearson r CSNK1D (CNV) vs. CSNK1D (RNASeq) r 0.6603 95% confidence interval 0.6233 to 0.6944 R squared 0.436 P value P (two-tailed) < 0.0001 P value summary **** Significant? (alpha = 0.05) Yes Number of XY Pairs 972 Table S2. TCGA RNA-seq and GISTIC2 copy number data for basal-like Pam50 breast tumors. Case ID CSNK1D (log2 CNV) CSNK1D (log2 RNASeq) TCGA-B6-A1KF-01-1.043 10.3646 TCGA-D8-A1JM-01-0.79 10.9116 TCGA-AN-A0FJ-01-0.564 10.8002 TCGA-BH-A18V-01-0.443 10.8238
TCGA-AR-A1AR-01-0.412 10.5239 TCGA-BH-A0E0-01 -0.399 10.9861 TCGA-AR-A1AY-01-0.393 11.3138 TCGA-E2-A150-01 -0.362 11.0116 TCGA-BH-A1F6-01 -0.358 11.0313 TCGA-B6-A0RU-01-0.341 11.0319 TCGA-E9-A22G-01-0.331 11.1134 TCGA-E2-A1LL-01-0.325 11.3173 TCGA-E2-A14X-01-0.315 10.9718 TCGA-A2-A0D0-01 -0.293 11.0423 TCGA-AO-A0JL-01-0.29 11.0765 TCGA-A1-A0SK-01-0.286 11.7043 TCGA-A2-A1G1-01 -0.263 11.1844 TCGA-A7-A26F-01-0.245 11.012 TCGA-E2-A1II-01-0.239 10.8081 TCGA-C8-A131-01 -0.203 11.2824 TCGA-E2-A159-01 -0.197 11.1713 TCGA-A2-A04U-01-0.16 10.7475 TCGA-AR-A1AJ-01-0.145 10.7918 TCGA-A2-A0SX-01-0.139 11.4065 TCGA-BH-A0E6-01 -0.126 11.4112 TCGA-BH-A0RX-01-0.121 11.1444 TCGA-AR-A2LR-01-0.103 11.1628 TCGA-E2-A1LI-01-0.063 11.0661 TCGA-AO-A124-01 -0.06 11.1313 TCGA-B6-A0I1-01 -0.047 12.0573 TCGA-E2-A1LG-01-0.047 10.9623 TCGA-A2-A0T2-01 -0.042 11.0656 TCGA-A8-A07U-01-0.028 11.31 TCGA-BH-A0DL-01-0.028 11.3668 TCGA-E2-A14N-01-0.025 10.9886 TCGA-A2-A25F-01-0.022 11.0767 TCGA-AN-A0FX-01-0.016 11.6719 TCGA-AO-A128-01 -0.015 11.2618 TCGA-AN-A0AT-01-0.013 11.4741 TCGA-EW-A1PB-01-0.006 11.5289 TCGA-B6-A0RT-01-0.002 11.9426 TCGA-EW-A1P8-01 0 11.5048 TCGA-A7-A13E-01 0.002 11.055 TCGA-AR-A256-01 0.005 11.2195 TCGA-A2-A0ST-01 0.006 11.6197 TCGA-A2-A0YJ-01 0.007 10.8807
TCGA-E2-A1LH-01 0.013 11.4122 TCGA-E9-A1N8-01 0.025 11.9359 TCGA-AQ-A04J-01 0.029 11.4846 TCGA-A2-A04Q-01 0.032 11.7329 TCGA-C8-A12K-01 0.032 11.295 TCGA-E9-A1ND-01 0.034 11.6336 TCGA-E9-A1N9-01 0.034 11.577 TCGA-AR-A0U0-01 0.036 11.1544 TCGA-B6-A0IJ-01 0.043 11.5088 TCGA-C8-A134-01 0.046 11.3199 TCGA-GM-A2DF-01 0.047 11.7215 TCGA-A7-A26I-01 0.049 10.801 TCGA-C8-A1HJ-01 0.05 10.9349 TCGA-AN-A0AL-01 0.053 11.5864 TCGA-AR-A0TP-01 0.057 11.1947 TCGA-AR-A1AH-01 0.064 11.7315 TCGA-AO-A12F-01 0.067 11.4088 TCGA-B6-A0WX-01 0.071 11.5309 TCGA-A7-A0DA-01 0.081 11.6348 TCGA-AR-A1AQ-01 0.084 11.5074 TCGA-AR-A0U1-01 0.089 11.5947 TCGA-A7-A0CE-01 0.102 11.6286 TCGA-E2-A158-01 0.106 11.65 TCGA-B6-A0IQ-01 0.117 11.77 TCGA-EW-A1OW-01 0.123 11.3132 TCGA-AR-A0TS-01 0.127 11.4598 TCGA-BH-A0AV-01 0.127 11.7347 TCGA-AR-A1AI-01 0.142 11.5158 TCGA-D8-A1JK-01 0.143 11.5229 TCGA-BH-A0BL-01 0.149 11.1747 TCGA-E2-A14Y-01 0.151 11.1147 TCGA-D8-A1XQ-01 0.169 11.4941 TCGA-E2-A1LK-01 0.177 11.3758 TCGA-A2-A0CM-01 0.197 11.5333 TCGA-BH-A0WA-01 0.201 11.5568 TCGA-AO-A129-01 0.202 11.7548 TCGA-D8-A27M-01 0.216 11.624 TCGA-A2-A0D2-01 0.232 11.7835 TCGA-AO-A0J4-01 0.237 11.3526 TCGA-E2-A1AZ-01 0.239 11.0279 TCGA-BH-A1F0-01 0.252 11.3959 TCGA-A1-A0SP-01 0.261 11.9585
TCGA-E9-A243-01 0.337 11.388 TCGA-C8-A12V-01 0.339 12.0051 TCGA-EW-A1PH-01 0.372 11.3175 TCGA-D8-A142-01 0.381 11.3717 TCGA-C8-A27B-01 0.4 11.3114 TCGA-BH-A18T-01 0.414 11.6526 TCGA-AR-A0U4-01 0.431 11.9696 TCGA-A8-A08R-01 0.455 11.623 TCGA-E9-A244-01 0.46 11.3525 TCGA-A8-A07O-01 0.477 11.6157 TCGA-GI-A2C9-01 0.493 11.6459 TCGA-D8-A143-01 0.546 11.7215 TCGA-AC-A2QH-01 0.569 11.7652 TCGA-D8-A27F-01 0.577 11.5589 TCGA-BH-A0BW-01 0.581 11.6911 TCGA-B6-A0RE-01 0.591 12.1321 TCGA-A7-A26G-01 0.594 11.4793 TCGA-BH-A1FC-01 0.637 11.8414 TCGA-D8-A27H-01 0.65 11.8682 TCGA-AO-A0J6-01 0.653 11.4469 TCGA-BH-A0BG-01 0.679 11.8266 TCGA-AR-A251-01 0.698 11.8978 TCGA-B6-A0X1-01 0.706 11.9575 TCGA-AN-A0FL-01 0.712 11.9925 TCGA-E2-A14R-01 0.72 11.2475 TCGA-D8-A1JL-01 0.727 12.1361 TCGA-A2-A0YM-01 0.733 11.4883 TCGA-AR-A24Q-01 0.734 11.4677 TCGA-A8-A07R-01 0.741 12.4764 TCGA-A1-A0SO-01 0.744 11.3751 TCGA-BH-A0B3-01 0.756 11.9527 TCGA-AN-A04D-01 0.779 11.8129 TCGA-B6-A0I2-01 0.83 12.1782 TCGA-HN-A2NL-01 0.884 12.2139 TCGA-AN-A0XU-01 0.916 12.3559 TCGA-A2-A04T-01 0.941 12.0598 TCGA-BH-A18Q-01 0.947 11.7939 TCGA-AO-A1KR-01 0.953 12.6042 TCGA-AC-A2BK-01 0.985 12.6516 TCGA-D8-A1XK-01 1.006 12.7212 TCGA-D8-A147-01 1.054 11.7882 TCGA-EW-A1P4-01 1.074 12.3612
TCGA-A7-A13D-01 1.082 11.998 TCGA-A2-A04P-01 1.182 11.8883 TCGA-A2-A0T0-01 1.287 12.2354 TCGA-BH-A18G-01 1.609 12.286 TCGA-A2-A0YE-01 2.131 13.3441 Parameter CSNK1D (CNV) vs. CSNK1D (RNASeq) Number of XY Pairs 135 Pearson r 0.7936 95% confidence interval 0.7213 to 0.8488 P value (two-tailed) < 0.0001 P value summary **** Is the correlation significant? (alpha=0.05) Yes R square 0.6298 Table S3. TCGA RNA-seq and GISTIC2 copy number data for HER2-positive Pam50 breast tumors. Case ID CSNK1D (log2 CNV) CSNK1D (log2 RNASeq) TCGA-D8-A1JA-01-0.815 10.3509 TCGA-A8-A07I-01-0.696 11.3485 TCGA-D8-A1XJ-01-0.658 11.0838 TCGA-C8-A12Z-01-0.639 11.4097 TCGA-B6-A0IK-01-0.583 11.3869 TCGA-A8-A08B-01-0.58 11.1066 TCGA-BH-A0EE-01-0.57 10.6764 TCGA-BH-A18R-01-0.551 10.9778 TCGA-BH-A1EV-01-0.547 11.2127 TCGA-E2-A152-01 -0.534 10.8425 TCGA-A8-A094-01 -0.511 10.7153 TCGA-BH-A1EN-01-0.51 11.0361 TCGA-EW-A1OV-01-0.438 11.2837 TCGA-E2-A14V-01-0.407 11.5734 TCGA-C8-A138-01 -0.398 11.3001 TCGA-A2-A0D1-01 -0.392 11.6464 TCGA-BH-A18P-01-0.332 11.6283 TCGA-C8-A12P-01-0.28 11.0356 TCGA-C8-A26X-01-0.26 11.3289 TCGA-AO-A12D-01-0.226 11.6768 TCGA-AC-A23H-01-0.167 11.4654
TCGA-D8-A13Z-01-0.158 11.5019 TCGA-A2-A04W-01-0.122 11.7519 TCGA-AR-A24U-01-0.09 11.4234 TCGA-A8-A08L-01-0.089 11.8631 TCGA-EW-A2FR-01-0.086 11.5808 TCGA-A2-A04X-01-0.07 11.4645 TCGA-E2-A14P-01-0.07 11.8421 TCGA-A8-A0A7-01 -0.046 11.5629 TCGA-A8-A09G-01-0.037 12.0441 TCGA-C8-A275-01 -0.004 11.4063 TCGA-C8-A12T-01-0.001 11.8839 TCGA-BH-A0B7-01 0.002 11.9312 TCGA-GM-A2DB-01 0.003 11.7265 TCGA-AR-A254-01 0.024 11.3669 TCGA-E9-A248-01 0.055 11.389 TCGA-E2-A1LB-01 0.062 12.1172 TCGA-A8-A08X-01 0.065 11.38 TCGA-AO-A0JE-01 0.07 11.4986 TCGA-GM-A2DH-01 0.071 11.5981 TCGA-B6-A0RH-01 0.079 11.8495 TCGA-D8-A1JG-01 0.109 11.7821 TCGA-E2-A1B0-01 0.122 11.3319 TCGA-D8-A1JF-01 0.163 11.6537 TCGA-A8-A09X-01 0.227 11.3593 TCGA-C8-A12Q-01 0.26 11.7751 TCGA-E9-A1RH-01 0.267 11.3578 TCGA-C8-A26Y-01 0.285 12.045 TCGA-B6-A0RS-01 0.306 11.5568 TCGA-A2-A0CX-01 0.363 11.7279 TCGA-B6-A0I9-01 0.401 12.4076 TCGA-AN-A0FV-01 0.415 12.2618 TCGA-C8-A1HK-01 0.451 12.0391 TCGA-A2-A0EQ-01 0.472 12.0048 TCGA-AR-A0TX-01 0.485 12.3589 TCGA-D8-A1XT-01 0.527 11.9042 TCGA-C8-A12L-01 0.577 11.7014 TCGA-C8-A1HF-01 0.606 11.7195 TCGA-BH-A203-01 0.852 12.2729 TCGA-AO-A0J2-01 0.934 12.3364 TCGA-AN-A04C-01 0.992 12.3203 TCGA-C8-A135-01 1.126 12.4547 TCGA-C8-A137-01 1.366 12.3692
TCGA-BH-A0AW-01 1.407 11.8353 TCGA-C8-A278-01 2.125 13.3421 TCGA-A2-A0T1-01 2.5 13.1671 TCGA-A8-A08J-01 3.657 13.3911 Parameter CSNK1D (CNV) vs. CSNK1D (RNASeq) Number of XY Pairs 67 Pearson r 0.8553 95% confidence interval 0.7741 to 0.9088 P value (two-tailed) < 0.0001 P value summary **** Is the correlation significant? (alpha=0.05) Yes R square 0.73156 Table S4. TCGA RNA-seq and GISTIC2 copy number data for luminal A Pam50 breast tumors. Case ID CSNK1D (log2 CNV) CSNK1D (log2 RNASeq) TCGA-E2-A156-01 -0.919 11.0154 TCGA-D8-A1JN-01-0.876 11.6467 TCGA-EW-A1J1-01 -0.828 11.5589 TCGA-A7-A0D9-01 -0.773 11.2158 TCGA-B6-A0IG-01-0.737 11.3643 TCGA-E9-A1RF-01-0.737 11.0847 TCGA-GM-A2D9-01 -0.728 11.2445 TCGA-BH-A0DZ-01-0.677 10.8932 TCGA-AO-A0J5-01 -0.647 11.2301 TCGA-D8-A27T-01-0.634 11.1288 TCGA-D8-A27V-01-0.615 10.8951 TCGA-B6-A0IE-01-0.613 11.2025 TCGA-E2-A15H-01-0.599 11.3348 TCGA-AN-A0FW-01-0.598 11.4859 TCGA-D8-A1XU-01-0.59 11.3962 TCGA-BH-A0BC-01-0.585 11.1423 TCGA-BH-A0B0-01 -0.547 10.7963 TCGA-BH-A1EY-01-0.503 10.8349 TCGA-EW-A1PA-01-0.489 9.1674 TCGA-GM-A2DA-01-0.488 11.3281 TCGA-AO-A03V-01-0.488 11.3542 TCGA-BH-A18F-01-0.479 11.0358
TCGA-AN-A0FD-01-0.479 11.6594 TCGA-AN-A04A-01-0.467 11.4649 TCGA-BH-A0HP-01-0.465 11.1104 TCGA-B6-A0RV-01-0.462 11.3354 TCGA-AR-A1AN-01-0.458 11.2867 TCGA-AR-A0U3-01 -0.431 10.7918 TCGA-E2-A14T-01-0.425 11.6371 TCGA-AN-A0AS-01-0.424 11.4479 TCGA-BH-A0BR-01-0.402 11.4581 TCGA-A7-A0CG-01-0.399 11.195 TCGA-AQ-A0Y5-01 -0.395 11.227 TCGA-BH-A0C1-01 -0.39 11.2753 TCGA-A2-A0CV-01-0.378 11.5556 TCGA-A8-A0AD-01-0.361 11.2773 TCGA-BH-A0DP-01-0.361 11.3385 TCGA-C8-A3M7-01 -0.351 11.2181 TCGA-C8-A132-01 -0.338 11.6064 TCGA-GI-A2C8-01 -0.332 11.7843 TCGA-A2-A259-01 -0.317 11.2675 TCGA-E9-A1NH-01-0.299 11.6303 TCGA-BH-A0BA-01-0.285 11.2389 TCGA-E2-A1B1-01 -0.281 10.8264 TCGA-B6-A0IH-01-0.255 11.8344 TCGA-BH-A1EU-01-0.245 11.2847 TCGA-AN-A046-01 -0.241 11.5057 TCGA-BH-A0B5-01 -0.234 11.531 TCGA-E2-A14Z-01-0.223 11.4609 TCGA-D8-A145-01 -0.213 11.7338 TCGA-BH-A18I-01-0.207 11.6137 TCGA-A7-A26E-01-0.206 11.474 TCGA-A7-A26H-01-0.2 11.3063 TCGA-BH-A1FH-01-0.195 11.3169 TCGA-GM-A2DI-01-0.142 11.5995 TCGA-AN-A0FT-01-0.132 11.3057 TCGA-E2-A15G-01-0.122 11.8392 TCGA-D8-A140-01 -0.121 11.4791 TCGA-BH-A0E9-01 -0.118 11.5636 TCGA-E2-A15M-01-0.11 11.0259 TCGA-E2-A1B5-01 -0.108 11.4169 TCGA-E2-A15E-01-0.097 11.7625 TCGA-C8-A273-01 -0.075 11.5462 TCGA-AN-A0XW-01-0.067 11.427
TCGA-AQ-A1H2-01 -0.062 11.6527 TCGA-A1-A0SQ-01-0.059 10.9441 TCGA-BH-A28Q-01-0.058 11.5877 TCGA-AC-A23E-01-0.055 11.4752 TCGA-GM-A2DN-01-0.054 11.7757 TCGA-A7-A3IZ-01-0.053 12.128 TCGA-E9-A2JT-01-0.05 11.7583 TCGA-A2-A0ER-01-0.05 11.3493 TCGA-E9-A1N4-01 -0.049 11.0719 TCGA-E2-A10B-01-0.045 11.5127 TCGA-D8-A27E-01-0.042 11.7528 TCGA-BH-A0EA-01-0.038 11.8117 TCGA-D8-A1XG-01-0.035 11.7851 TCGA-EW-A2FS-01-0.034 11.5087 TCGA-E2-A14Q-01-0.034 11.7187 TCGA-AO-A0JI-01-0.033 11.3763 TCGA-A2-A0CS-01-0.031 11.83 TCGA-BH-A0DX-01-0.031 11.0685 TCGA-D8-A1XO-01-0.027 11.498 TCGA-A7-A0CH-01-0.025 11.5348 TCGA-A2-A0ES-01-0.025 11.6 TCGA-BH-A0BJ-01-0.024 11.7699 TCGA-AO-A12A-01-0.023 11.5117 TCGA-A2-A0CQ-01-0.021 11.7208 TCGA-E2-A1IL-01-0.02 12.023 TCGA-B6-A0IA-01-0.02 11.1448 TCGA-E2-A1L9-01 -0.02 11.1766 TCGA-BH-A0EI-01-0.02 11.6112 TCGA-AN-A0FS-01-0.02 11.8361 TCGA-AN-A0XP-01-0.019 11.7936 TCGA-BH-A201-01 -0.018 11.5462 TCGA-E2-A15P-01-0.018 11.8986 TCGA-D8-A1JS-01-0.018 11.4209 TCGA-BH-A0HI-01-0.018 11.6638 TCGA-BH-A0DO-01-0.018 11.7144 TCGA-A2-A0EM-01-0.017 11.6584 TCGA-E9-A3Q9-01 -0.017 11.5679 TCGA-E2-A1BC-01-0.017 11.5242 TCGA-B6-A0WT-01-0.017 11.5238 TCGA-D8-A27G-01-0.016 11.8193 TCGA-A1-A0SF-01-0.015 11.8572 TCGA-D8-A1XC-01-0.015 11.6828
TCGA-A2-A3KD-01-0.015 11.6727 TCGA-AO-A12G-01-0.014 11.5954 TCGA-BH-A0DQ-01-0.013 11.6116 TCGA-BH-A0H9-01 -0.013 12.0772 TCGA-C8-A1HE-01-0.013 11.5783 TCGA-E9-A1N5-01 -0.012 11.7208 TCGA-A7-A3J1-01 -0.011 12.1132 TCGA-A8-A09V-01-0.011 11.7336 TCGA-AR-A24M-01-0.011 11.1732 TCGA-E9-A1R0-01 -0.01 12.0081 TCGA-A2-A0YI-01-0.01 11.818 TCGA-A8-A0A1-01 -0.009 11.5289 TCGA-AR-A24W-01-0.009 11.5911 TCGA-A1-A0SE-01-0.008 11.6774 TCGA-E2-A15I-01-0.008 11.975 TCGA-A7-A3IY-01-0.008 11.8274 TCGA-A2-A3KC-01-0.007 11.7434 TCGA-BH-A0BM-01-0.007 11.2484 TCGA-AR-A1AL-01-0.007 11.6067 TCGA-AC-A23C-01-0.007 11.099 TCGA-BH-A0BQ-01-0.007 11.6318 TCGA-E9-A1RD-01-0.006 11.4992 TCGA-A8-A0A4-01 -0.006 11.5275 TCGA-B6-A0RO-01-0.005 10.8708 TCGA-A7-A13G-01-0.005 11.8121 TCGA-D8-A1JU-01-0.004 11.5369 TCGA-GM-A2DM-01-0.004 11.9069 TCGA-BH-A18K-01-0.004 11.4408 TCGA-D8-A1XD-01-0.004 11.9255 TCGA-AR-A0TR-01-0.004 11.8997 TCGA-B6-A0IC-01-0.004 11.9687 TCGA-D8-A27L-01-0.004 11.883 TCGA-AR-A24T-01-0.004 11.5315 TCGA-AC-A2FG-01-0.003 11.8846 TCGA-A2-A0D3-01 -0.003 11.7123 TCGA-C8-A133-01 -0.003 11.7409 TCGA-B6-A0I5-01 -0.003 11.557 TCGA-B6-A0X0-01 -0.003 11.8499 TCGA-B6-A0X4-01 -0.002 11.7033 TCGA-E9-A245-01 -0.002 12.0704 TCGA-AO-A0J8-01 -0.002 11.9023 TCGA-D8-A1XA-01-0.002 12.0245
TCGA-D8-A27K-01-0.002 11.6865 TCGA-B6-A0IP-01-0.002 12.1183 TCGA-EW-A1J3-01 -0.002 11.1423 TCGA-BH-A0DV-01-0.001 11.4264 TCGA-BH-A0H3-01 -0.001 11.6893 TCGA-C8-A12Y-01-0.001 11.4211 TCGA-E2-A1IK-01-0.001 11.8084 TCGA-AO-A0JF-01-0.001 11.5047 TCGA-AO-A12H-01-0.001 11.9181 TCGA-A2-A0YD-01 0 11.6167 TCGA-BH-A0DS-01 0 11.4654 TCGA-AN-A0XV-01 0 11.4873 TCGA-BH-A0BO-01 0 12.2957 TCGA-AQ-A04L-01 0 11.6593 TCGA-BH-A0GZ-01 0 11.8576 TCGA-BH-A1FL-01 0 12.0912 TCGA-BH-A1FR-01 0 11.9702 TCGA-E9-A1RC-01 0 11.7807 TCGA-A8-A083-01 0 11.6224 TCGA-AR-A0TW-01 0.001 12.0947 TCGA-A2-A0T5-01 0.001 11.5058 TCGA-B6-A0WS-01 0.001 11.4545 TCGA-EW-A1IX-01 0.001 11.874 TCGA-D8-A1JH-01 0.002 11.6454 TCGA-EW-A1PE-01 0.002 11.4538 TCGA-AR-A24O-01 0.002 11.4428 TCGA-AN-A0FK-01 0.003 11.6233 TCGA-D8-A1XV-01 0.003 11.4035 TCGA-BH-A0H5-01 0.003 11.8281 TCGA-B6-A0WZ-01 0.003 11.41 TCGA-D8-A27P-01 0.003 11.8028 TCGA-A8-A091-01 0.004 12.0792 TCGA-AC-A3OD-01 0.004 11.9735 TCGA-BH-A1FB-01 0.004 11.6132 TCGA-A2-A1FZ-01 0.004 11.4407 TCGA-E2-A15R-01 0.004 11.6117 TCGA-E2-A1IO-01 0.005 11.9329 TCGA-AO-A125-01 0.005 11.4683 TCGA-BH-A0HK-01 0.005 11.2696 TCGA-EW-A2FV-01 0.005 11.4251 TCGA-AO-A126-01 0.005 11.873 TCGA-E9-A1NG-01 0.005 11.2439
TCGA-A2-A0EW-01 0.005 11.7735 TCGA-E2-A1L8-01 0.006 11.6199 TCGA-D8-A27I-01 0.006 11.7076 TCGA-E2-A1L6-01 0.006 11.551 TCGA-AN-A0FN-01 0.006 11.3007 TCGA-BH-A0E1-01 0.006 11.2788 TCGA-AC-A2B8-01 0.006 11.5121 TCGA-AR-A1AU-01 0.006 11.7411 TCGA-AR-A2LO-01 0.006 12.0262 TCGA-D8-A141-01 0.007 11.504 TCGA-BH-A0HO-01 0.007 11.3596 TCGA-E2-A15J-01 0.007 11.7208 TCGA-A8-A08Z-01 0.007 11.605 TCGA-AC-A2FF-01 0.007 11.5213 TCGA-BH-A0BS-01 0.007 11.4787 TCGA-AR-A2LM-01 0.008 11.6969 TCGA-BH-A0EB-01 0.008 11.7497 TCGA-E9-A227-01 0.008 11.4565 TCGA-A7-A0DB-01 0.009 11.8564 TCGA-D8-A1X8-01 0.009 11.6167 TCGA-A2-A0T4-01 0.01 11.664 TCGA-EW-A1IW-01 0.01 11.1387 TCGA-BH-A0W4-01 0.01 11.8021 TCGA-A2-A0EO-01 0.01 11.9303 TCGA-E9-A229-01 0.011 11.6461 TCGA-E9-A1N3-01 0.012 11.8685 TCGA-BH-A0DT-01 0.012 11.5833 TCGA-A8-A07J-01 0.012 11.7786 TCGA-BH-A0DH-01 0.012 10.9333 TCGA-A2-A0YL-01 0.012 11.4918 TCGA-AO-A03M-01 0.013 12.0547 TCGA-E2-A1IF-01 0.013 11.8029 TCGA-AO-A0JC-01 0.013 11.4188 TCGA-E2-A1IU-01 0.013 11.7282 TCGA-BH-A2L8-01 0.014 12.0419 TCGA-BH-A0W5-01 0.014 11.8119 TCGA-E9-A24A-01 0.014 11.4805 TCGA-E2-A10E-01 0.015 11.6855 TCGA-A8-A07F-01 0.015 11.2929 TCGA-E2-A154-01 0.015 11.7525 TCGA-BH-A0GY-01 0.015 11.8592 TCGA-BH-A1ET-01 0.015 11.3871