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Table 3 Annotation and expression correlation for select K2p methylation loci associated with triple negative subtype

From: Associations of two-pore domain potassium channels and triple negative breast cancer subtype in The Cancer Genome Atlas: systematic evaluation of gene expression and methylation

Gene GLM Modelsa Annotationb Luminal Ac Combined triple negativec
CpG loci Beta p-value N Rho p-value N Rho p-value
KCNK1
 cg17851113 0.188 1.45E−12   339 0.487 1.31E−21 103 0.301 2.02E−03
 cg23054119 −0.140 3.40E−06   338 0.498 1.37E−22 103 0.114 2.53E−01
KCNK2
 cg04923840 −0.219 2.00E−25 Body 339 0.227 2.52E−05 103 0.253 9.81E−03
 cg06873024 −0.183 1.64E−21 Between CENPF/KCNK2 339 0.124 2.21E−02 103 0.241 1.43E−02
 cg24464500 −0.206 9.81E−20 Body 337 0.280 1.70E−07 103 −0.048 6.33E−01
 cg13916421 0.085 1.53E−11 Body 339 0.061 2.60E−01 103 0.211 3.22E−02
 cg00848374 0.129 2.35E−07 1stExon; 5′UTR 338 0.202 1.83E−04 103 −0.079 4.27E−01
KCNK3
 cg20491914 −0.170 2.97E−11 TSS1500 339 0.297 2.46E−08 103 −0.164 9.82E−02
 cg11273176 −0.128 1.60E−10 Body 339 0.388 1.23E−13 103 0.408 1.88E−05
 cg06854842 −0.090 2.20E−09 Body 339 0.360 7.91E−12 103 0.451 1.78E−06
 cg05616379 0.078 1.50E−06 Body 339 0.221 3.97E−05 103 0.452 1.64E−06
KCNK4
 cg01708924 −0.185 2.87E−31 3′UTR PRDX5 339 0.221 3.92E−05 103 0.017 8.68E−01
 cg10718809 −0.148 2.81E−23 PRDX5: body 339 0.224 3.04E−05 103 −0.026 7.98E−01
 cg10155572 −0.037 1.92E−07 ESRRA: body 339 0.239 8.75E−06 103 −0.001 9.92E−01
KCNK5
 cg05255811 −0.373 9.32E−70 Body 339 0.369 2.40E−12 103 0.674 5.95E−15
 cg18705155 −0.226 2.71E−26 Body 339 −0.120 2.78E−02 103 0.605 1.33E−11
 cg09130674 −0.224 1.52E−25 Body 339 −0.197 2.65E−04 103 0.711 3.91E−17
 cg21388745 −0.119 1.81E−23 Body 339 0.203 1.68E−04 103 0.701 1.59E−16
 cg00859574 −0.129 4.14E−08 Body 339 −0.160 3.04E−03 103 0.430 5.90E−06
 cg02128567 −0.113 3.53E−07 1stExon; 5′UTR 339 0.253 2.35E−06 103 0.345 3.62E−04
KCNK6
 cg13521973 0.039 6.36E−07 Body 339 0.244 5.62E−06 103 −0.193 5.07E−02
 cg08216899 −0.025 5.10E−06 3′UTR 339 0.110 4.25E−02 103 0.217 2.75E−02
KCNK7
 cg10142520 −0.210 3.27E−22 EHBP1L1 body 339 0.215 6.77E−05 103 0.014 8.90E−01
 cg17290213 −0.126 1.09E−17 EHBP1L1 body 339 0.223 3.57E−05 103 0.092 3.55E−01
 cg03416228 −0.092 6.06E−15 Between EHBP1L1/KCNK7 339 0.225 2.91E−05 103 −0.171 8.44E−02
 cg12758867 −0.072 2.02E−14 EHBP1L1 body 339 0.223 3.49E−05 103 0.095 3.38E−01
 cg13179915 −0.067 3.13E−11 1stExon 339 0.205 1.39E−04 103 0.305 1.75E−03
 cg05436845 −0.036 6.28E−06 MAP3K11: body 339 0.223 3.34E−05 103 0.045 6.51E−01
 cg17918700 −0.030 1.55E−05 TSS200 339 0.230 1.84E−05 103 0.277 4.55E−03
KCNK9
 cg21415530 −0.332 1.14E−56 TSS1500 339 −0.159 3.32E−03 103 0.383 6.39E−05
 cg12175729 −0.273 6.23E−22 TSS1500 339 −0.056 3.02E−01 103 0.215 2.88E−02
 cg20761810 0.155 1.67E−16 Between KCNK9/TRAPPC9 339 0.238 9.24E−06 103 −0.119 2.30E−01
 cg05988964 0.183 2.15E−11 3′UTR 339 0.208 1.16E−04 103 0.197 4.56E−02
 cg17336929 −0.110 9.79E−10 Between KCNK9/TRAPPC9 339 0.055 3.13E−01 103 0.248 1.17E−02
 cg25900813 −0.106 4.38E−08 Between KCNK9/TRAPPC9 339 0.069 2.07E−01 103 0.236 1.62E−02
 cg24020826 0.102 7.26E−08 3′UTR 339 0.176 1.12E−03 103 0.204 3.84E−02
 cg18195416 0.125 6.90E−06 Between COL22A1/KCNK9 339 0.206 1.29E−04 103 0.237 1.60E−02
 cg03919980 −0.066 2.96E−05 Between KCNK9/TRAPPC9 339 0.114 3.59E−02 103 0.222 2.43E−02
KCNK10
 cg09945147 0.219 3.03E−33 Between GPR65/KCNK10 339 0.241 7.35E−06 103 0.312 1.32E−03
 cg01733928 0.153 4.71E−29 Between GPR65/KCNK10 339 0.250 3.17E−06 103 0.282 3.97E−03
 cg08069902 0.190 9.47E−26 Body 339 0.088 1.07E−01 103 0.231 1.90E−02
 cg02222791 0.225 1.04E−23 Between GPR65/KCNK10 339 0.238 9.06E−06 103 0.267 6.42E−03
 cg18078958 0.219 2.22E−20 Between GPR65/KCNK10 339 0.181 8.11E−04 103 0.290 2.94E−03
 cg10172979 0.123 1.23E−14 Between GPR65/KCNK10 339 0.167 2.01E−03 103 0.286 3.40E−03
 cg24740404 0.167 1.05E−13 Between GPR65/KCNK10 339 0.166 2.12E−03 103 0.211 3.21E−02
 cg15347348 0.134 2.77E−13 Body; TSS1500 339 0.118 2.99E−02 103 0.313 1.27E−03
 cg19453093 0.081 3.20E−12 Body 339 0.205 1.46E−04 103 0.375 9.54E−05
 cg19476426 0.145 2.58E−11 Between GPR65/KCNK10 339 0.172 1.44E−03 103 0.212 3.16E−02
 cg15493607 0.167 4.53E−11 Body; TSS1500 339 0.197 2.64E−04 103 0.313 1.29E−03
 cg17671157 −0.105 6.87E−10 1stExon; 5′UTR 337 −0.068 2.10E−01 103 0.229 1.97E−02
 cg18525616 0.144 8.98E−10 Between GPR65/KCNK10 339 0.156 4.04E−03 103 0.270 5.81E−03
 cg00927624 0.143 3.91E−09 Between KCNK10/SPATA7 339 0.249 3.43E−06 103 0.318 1.08E−03
 cg23291854 −0.107 4.26E−08 1stExon; 5′UTR 339 −0.040 4.65E−01 103 0.282 3.85E−03
 cg22521269 −0.093 1.35E−06 TSS200 339 −0.116 3.35E−02 103 0.215 2.89E−02
 cg02883668 0.079 2.03E−05 Body 339 0.177 1.07E−03 103 0.262 7.40E−03
 cg23381267 0.097 6.14E−05 Body 339 0.154 4.44E−03 103 0.227 2.11E−02
KCNK12
 cg00981060 0.183 1.55E−20 Between MSH2/KCNK12 339 0.073 1.79E−01 103 0.223 2.38E−02
 cg27138584 −0.059 4.47E−05 Body 339 0.003 9.63E−01 103 0.258 8.46E−03
 cg00783525 0.054 7.26E−05 Body 339 0.113 3.70E−02 103 0.335 5.39E−04
KCNK13
 cg21191365 −0.209 2.20E−20 Body 339 −0.026 6.39E−01 103 0.201 4.17E−02
 cg00364611 −0.118 1.32E−11 1stExon 339 −0.170 1.66E−03 103 0.275 4.87E−03
 cg25225073 −0.100 4.05E−07 Body 339 0.073 1.80E−01 103 0.303 1.88E−03
KCNK15
 cg13598409 0.210 1.39E−56 TSS1500 339 0.251 2.87E−06 103 0.093 3.50E−01
 cg04966972 0.164 7.67E−45 TSS1500 339 0.298 2.14E−08 103 0.078 4.35E−01
 cg11681959 0.109 5.52E−28 TSS200 339 0.278 2.01E−07 103 −0.053 5.98E−01
 cg25301532 −0.113 6.12E−09 Body 339 0.253 2.35E−06 103 0.290 2.99E−03
 cg09357268 −0.048 4.75E−08 Body 339 0.195 2.96E−04 103 0.225 2.24E−02
KCNK16
 cg05897803 0.114 3.86E−11 TSS200 339 0.342 1.04E−10 103 0.009 9.28E−01
 cg07970874 0.087 2.82E−06 TSS200 339 0.269 4.73E−07 103 0.019 8.47E−01
KCNK17
 cg13855924 −0.142 2.45E−12 Body 339 0.209 1.09E−04 103 −0.105 2.93E−01
 cg04755571 −0.131 5.17E−10 TSS200 339 0.241 7.29E−06 103 0.262 7.62E−03
 cg06347083 −0.124 5.92E−10 TSS200 339 0.215 6.61E−05 103 0.216 2.82E−02
 cg10712551 −0.122 1.58E−07 Body 339 −0.175 1.19E−03 103 0.239 1.49E−02
 cg03252829 −0.105 1.61E−05 1stExon; 5′UTR 339 0.284 1.04E−07 103 0.200 4.28E−02
 cg08315770 −0.103 6.55E−05 1stExon 339 0.205 1.48E−04 103 −0.084 4.02E−01
  1. mRNA expression z-scores (RNA Seq V2 RSEM)
  2. Spearman’s Rho values of <0.2 or >0.2 were considered evidence of correlation if also associated with p-values <0.05 (these values are in italics)
  3. K2p 2-pore domain K+ channel genes, glm generalized linear model
  4. aAge and race adjusted associations of individual methylated CpG loci and combined triple negative vs. luminal A subtype were ranked according to p-value (smallest first) and all significant loci were selected for further evaluation (Bonferroni adjusted threshold for methylation analyses = p < 8.22 × 10(−8))
  5. bAnnotation data obtained from Illumina for Human Methylation 450K chip array (http://support.illumina.com/array/array_kits/infinium_humanmethylation450_beadchip_kit/downloads.html)
  6. cFunctional correlation between methylation and expression was then examined using Spearman’s correlation and results are presented stratified by subtype