The Beta value indicates level of DNA methylation ranging from 0 (unmethylated) to 1 (fully methylated). Different beta value cut-off has been considered to indicate hyper-methylation [Beta value: 0.7 - 0.5] or hypo-methylation [Beta-value: 0.3 - 0.25]. PMID: 29027401, 23291739
PROBES
CLICK TO SEE PROBE LIST. Please note that the Beta value is the ratio of the methylated probe intensity and the sum of methylated and unmethylated probe intensity. Beta value ranges from 0 to 1. The above boxplot represents beta values of CpG probes located upto 1500bp upstream of gene's start site [TSS200, TSS1500]
Illumina Id
RefGene_group
cg03575666
TSS1500
cg01495122
TSS200
cg00930833
TSS1500
cg17816908
TSS200
cg24319902
TSS200
cg04255616
TSS1500
cg21517947
TSS200
cg07122178
TSS1500
cg07935886
TSS1500
cg01074584
TSS1500
cg10406295
TSS200
cg00000321
TSS1500
cg09410389
TSS1500
cg23359714
TSS1500
cg06166767
TSS1500
cg14824386
TSS1500
cg14904908
TSS1500
cg03133371
TSS1500
Comparison
Statistical significance
Normal-vs-Primary
<1E-12
The Beta value indicates level of DNA methylation ranging from 0 (unmethylated) to 1 (fully methylated). Different beta value cut-off has been considered to indicate hyper-methylation [Beta value: 0.7 - 0.5] or hypo-methylation [Beta-value: 0.3 - 0.25]. PMID: 29027401, 23291739
PROBES
CLICK TO SEE PROBE LIST. Please note that the Beta value is the ratio of the methylated probe intensity and the sum of methylated and unmethylated probe intensity. Beta value ranges from 0 to 1. The above boxplot represents beta values of CpG probes located upto 1500bp upstream of gene's start site [TSS200, TSS1500]
NOTEa
Cancer stage information is not available for 7 samples.
Illumina Id
RefGene_group
cg03575666
TSS1500
cg01495122
TSS200
cg00930833
TSS1500
cg17816908
TSS200
cg24319902
TSS200
cg04255616
TSS1500
cg21517947
TSS200
cg07122178
TSS1500
cg07935886
TSS1500
cg01074584
TSS1500
cg10406295
TSS200
cg00000321
TSS1500
cg09410389
TSS1500
cg23359714
TSS1500
cg06166767
TSS1500
cg14824386
TSS1500
cg14904908
TSS1500
cg03133371
TSS1500
Show statistics
Hide statistics
Comparison
Statistical significance
Normal-vs-Stage1
8.62470095341905E-11
Normal-vs-Stage2
1.62436730732907E-12
Normal-vs-Stage3
<1E-12
Normal-vs-Stage4
9.95059999999715E-05
Stage1-vs-Stage2
2.685200E-01
Stage1-vs-Stage3
9.724200E-02
Stage1-vs-Stage4
9.128000E-01
Stage2-vs-Stage3
3.821800E-01
Stage2-vs-Stage4
6.387000E-01
Stage3-vs-Stage4
4.755800E-01
The Beta value indicates level of DNA methylation ranging from 0 (unmethylated) to 1 (fully methylated). Different beta value cut-off has been considered to indicate hyper-methylation [Beta value: 0.7 - 0.5] or hypo-methylation [Beta-value: 0.3 - 0.25]. PMID: 29027401, 23291739
PROBES
CLICK TO SEE PROBE LIST. Please note that the Beta value is the ratio of the methylated probe intensity and the sum of methylated and unmethylated probe intensity. Beta value ranges from 0 to 1. The above boxplot represents beta values of CpG probes located upto 1500bp upstream of gene's start site [TSS200, TSS1500]
NOTEa
Patient race information is not available for 16 samples. One sample from American Indians are not considered in the above plot
Illumina Id
RefGene_group
cg03575666
TSS1500
cg01495122
TSS200
cg00930833
TSS1500
cg17816908
TSS200
cg24319902
TSS200
cg04255616
TSS1500
cg21517947
TSS200
cg07122178
TSS1500
cg07935886
TSS1500
cg01074584
TSS1500
cg10406295
TSS200
cg00000321
TSS1500
cg09410389
TSS1500
cg23359714
TSS1500
cg06166767
TSS1500
cg14824386
TSS1500
cg14904908
TSS1500
cg03133371
TSS1500
Show statistics
Hide statistics
Comparison
Statistical significance
Normal-vs-Caucasian
<1E-12
Normal-vs-AfricanAmerican
1.0325074129014E-14
Normal-vs-Asian
2.59400000035548E-07
Caucasian-vs-AfricanAmerican
8.225800E-01
Caucasian-vs-Asian
1.410760E-01
AfricanAmerican-vs-Asian
2.417800E-01
The Beta value indicates level of DNA methylation ranging from 0 (unmethylated) to 1 (fully methylated). Different beta value cut-off has been considered to indicate hyper-methylation [Beta value: 0.7 - 0.5] or hypo-methylation [Beta-value: 0.3 - 0.25]. PMID: 29027401, 23291739
PROBES
CLICK TO SEE PROBE LIST. Please note that the Beta value is the ratio of the methylated probe intensity and the sum of methylated and unmethylated probe intensity. Beta value ranges from 0 to 1. The above boxplot represents beta values of CpG probes located upto 1500bp upstream of gene's start site [TSS200, TSS1500]
NOTEa
Patient gender information is not available for 1 sample.
Illumina Id
RefGene_group
cg03575666
TSS1500
cg01495122
TSS200
cg00930833
TSS1500
cg17816908
TSS200
cg24319902
TSS200
cg04255616
TSS1500
cg21517947
TSS200
cg07122178
TSS1500
cg07935886
TSS1500
cg01074584
TSS1500
cg10406295
TSS200
cg00000321
TSS1500
cg09410389
TSS1500
cg23359714
TSS1500
cg06166767
TSS1500
cg14824386
TSS1500
cg14904908
TSS1500
cg03133371
TSS1500
Show statistics
Hide statistics
Comparison
Statistical significance
Normal-vs-Male
8.895400E-03
Normal-vs-Female
1.62447832963153E-12
Male-vs-Female
5.188500E-02
The Beta value indicates level of DNA methylation ranging from 0 (unmethylated) to 1 (fully methylated). Different beta value cut-off has been considered to indicate hyper-methylation [Beta value: 0.7 - 0.5] or hypo-methylation [Beta-value: 0.3 - 0.25]. PMID: 29027401, 23291739
PROBES
CLICK TO SEE PROBE LIST. Please note that the Beta value is the ratio of the methylated probe intensity and the sum of methylated and unmethylated probe intensity. Beta value ranges from 0 to 1. The above boxplot represents beta values of CpG probes located upto 1500bp upstream of gene's start site [TSS200, TSS1500]
NOTEa
Patient age information is not available for 2 samples.
Illumina Id
RefGene_group
cg03575666
TSS1500
cg01495122
TSS200
cg00930833
TSS1500
cg17816908
TSS200
cg24319902
TSS200
cg04255616
TSS1500
cg21517947
TSS200
cg07122178
TSS1500
cg07935886
TSS1500
cg01074584
TSS1500
cg10406295
TSS200
cg00000321
TSS1500
cg09410389
TSS1500
cg23359714
TSS1500
cg06166767
TSS1500
cg14824386
TSS1500
cg14904908
TSS1500
cg03133371
TSS1500
Show statistics
Hide statistics
Comparison
Statistical significance
Normal-vs-Age(21-40Yrs)
1.47499999991751E-07
Normal-vs-Age(41-60Yrs)
1.62458935193399E-12
Normal-vs-Age(61-80Yrs)
<1E-12
Normal-vs-Age(81-100Yrs)
2.21309999999253E-05
Age(21-40Yrs)-vs-Age(41-60Yrs)
8.830800E-01
Age(21-40Yrs)-vs-Age(61-80Yrs)
2.438100E-02
Age(21-40Yrs)-vs-Age(81-100Yrs)
1.180430E-01
Age(41-60Yrs)-vs-Age(61-80Yrs)
3.968300E-04
Age(41-60Yrs)-vs-Age(81-100Yrs)
7.748400E-02
Age(61-80Yrs)-vs-Age(81-100Yrs)
8.485800E-01
The Beta value indicates level of DNA methylation ranging from 0 (unmethylated) to 1 (fully methylated). Different beta value cut-off has been considered to indicate hyper-methylation [Beta value: 0.7 - 0.5] or hypo-methylation [Beta-value: 0.3 - 0.25]. PMID: 29027401, 23291739
PROBES
CLICK TO SEE PROBE LIST. Please note that the Beta value is the ratio of the methylated probe intensity and the sum of methylated and unmethylated probe intensity. Beta value ranges from 0 to 1. The above boxplot represents beta values of CpG probes located upto 1500bp upstream of gene's start site [TSS200, TSS1500]
Illumina Id
RefGene_group
cg03575666
TSS1500
cg01495122
TSS200
cg00930833
TSS1500
cg17816908
TSS200
cg24319902
TSS200
cg04255616
TSS1500
cg21517947
TSS200
cg07122178
TSS1500
cg07935886
TSS1500
cg01074584
TSS1500
cg10406295
TSS200
cg00000321
TSS1500
cg09410389
TSS1500
cg23359714
TSS1500
cg06166767
TSS1500
cg14824386
TSS1500
cg14904908
TSS1500
cg03133371
TSS1500
Show statistics
Hide statistics
Comparison
Statistical significance
Normal-vs-N0
1.62447832963153E-12
Normal-vs-N1
1.62436730732907E-12
Normal-vs-N2
4.43756142942675E-13
Normal-vs-N3
1.93439997353551E-09
N0-vs-N1
6.510200E-01
N0-vs-N2
1.864370E-01
N0-vs-N3
3.214600E-01
N1-vs-N2
1.134030E-01
N1-vs-N3
2.205400E-01
N2-vs-N3
9.385400E-01
The Beta value indicates level of DNA methylation ranging from 0 (unmethylated) to 1 (fully methylated). Different beta value cut-off has been considered to indicate hyper-methylation [Beta value: 0.7 - 0.5] or hypo-methylation [Beta-value: 0.3 - 0.25]. PMID: 29027401, 23291739
PROBES
CLICK TO SEE PROBE LIST. Please note that the Beta value is the ratio of the methylated probe intensity and the sum of methylated and unmethylated probe intensity. Beta value ranges from 0 to 1. The above boxplot represents beta values of CpG probes located upto 1500bp upstream of gene's start site [TSS200, TSS1500]
Illumina Id
RefGene_group
cg03575666
TSS1500
cg01495122
TSS200
cg00930833
TSS1500
cg17816908
TSS200
cg24319902
TSS200
cg04255616
TSS1500
cg21517947
TSS200
cg07122178
TSS1500
cg07935886
TSS1500
cg01074584
TSS1500
cg10406295
TSS200
cg00000321
TSS1500
cg09410389
TSS1500
cg23359714
TSS1500
cg06166767
TSS1500
cg14824386
TSS1500
cg14904908
TSS1500
cg03133371
TSS1500
Show statistics
Hide statistics
Comparison
Statistical significance
Normal-vs-IDC
<1E-12
Normal-vs-ILC
1.11022302462516E-16
Normal-vs-Mixed
1.136930E-03
Normal-vs-Other
4.183300E-04
Normal-vs-Mucinous
8.903200E-03
Normal-vs-Metaplastic
4.169600E-02
Normal-vs-INOS
N/A
Normal-vs-Medullary
3.6268000000006E-05
IDC-vs-ILC
1.199420E-01
IDC-vs-Mixed
8.238400E-01
IDC-vs-Other
8.080200E-01
IDC-vs-Mucinous
8.855400E-01
IDC-vs-Metaplastic
2.133600E-01
IDC-vs-INOS
N/A
IDC-vs-Medullary
7.645200E-01
ILC-vs-Mixed
3.579600E-01
ILC-vs-Other
3.130600E-01
ILC-vs-Mucinous
4.875800E-01
ILC-vs-Metaplastic
5.598000E-02
ILC-vs-INOS
N/A
ILC-vs-Medullary
9.889400E-01
Mixed-vs-Other
9.932000E-01
Mixed-vs-Mucinous
9.809000E-01
Mixed-vs-Metaplastic
2.771800E-01
Mixed-vs-INOS
N/A
Mixed-vs-Medullary
6.752600E-01
Other-vs-Mucinous
9.869600E-01
Other-vs-Metaplastic
2.989200E-01
Other-vs-INOS
N/A
Other-vs-Medullary
6.985800E-01
Mucinous-vs-Metaplastic
2.740600E-01
Mucinous-vs-INOS
N/A
Mucinous-vs-Medullary
6.827000E-01
Metaplastic-vs-INOS
N/A
Metaplastic-vs-Medullary
1.330630E-01
INOS-vs-Medullary
N/A
The Beta value indicates level of DNA methylation ranging from 0 (unmethylated) to 1 (fully methylated). Different beta value cut-off has been considered to indicate hyper-methylation [Beta value: 0.7 - 0.5] or hypo-methylation [Beta-value: 0.3 - 0.25]. PMID: 29027401, 23291739
PROBES
CLICK TO SEE PROBE LIST. Please note that the Beta value is the ratio of the methylated probe intensity and the sum of methylated and unmethylated probe intensity. Beta value ranges from 0 to 1. The above boxplot represents beta values of CpG probes located upto 1500bp upstream of gene's start site [TSS200, TSS1500]
Illumina Id
RefGene_group
cg03575666
TSS1500
cg01495122
TSS200
cg00930833
TSS1500
cg17816908
TSS200
cg24319902
TSS200
cg04255616
TSS1500
cg21517947
TSS200
cg07122178
TSS1500
cg07935886
TSS1500
cg01074584
TSS1500
cg10406295
TSS200
cg00000321
TSS1500
cg09410389
TSS1500
cg23359714
TSS1500
cg06166767
TSS1500
cg14824386
TSS1500
cg14904908
TSS1500
cg03133371
TSS1500
Show statistics
Hide statistics
Comparison
Statistical significance
Normal-vs-Luminal
<1E-12
Normal-vs-HER2Positive
6.322200E-02
Normal-vs-TNBC
2.68296496130915E-12
Luminal-vs-HER2Positive
5.222200E-01
Luminal-vs-TNBC
5.880600E-01
HER2Positive-vs-TNBC
7.162800E-01
The Beta value indicates level of DNA methylation ranging from 0 (unmethylated) to 1 (fully methylated). Different beta value cut-off has been considered to indicate hyper-methylation [Beta value: 0.7 - 0.5] or hypo-methylation [Beta-value: 0.3 - 0.25]. PMID: 29027401, 23291739
PROBES
CLICK TO SEE PROBE LIST. Please note that the Beta value is the ratio of the methylated probe intensity and the sum of methylated and unmethylated probe intensity. Beta value ranges from 0 to 1. The above boxplot represents beta values of CpG probes located upto 1500bp upstream of gene's start site [TSS200, TSS1500]
Illumina Id
RefGene_group
cg03575666
TSS1500
cg01495122
TSS200
cg00930833
TSS1500
cg17816908
TSS200
cg24319902
TSS200
cg04255616
TSS1500
cg21517947
TSS200
cg07122178
TSS1500
cg07935886
TSS1500
cg01074584
TSS1500
cg10406295
TSS200
cg00000321
TSS1500
cg09410389
TSS1500
cg23359714
TSS1500
cg06166767
TSS1500
cg14824386
TSS1500
cg14904908
TSS1500
cg03133371
TSS1500
Show statistics
Hide statistics
Comparison
Statistical significance
Normal-vs-Pre-menopause
3.07742720195847E-12
Normal-vs-Peri-menopause
2.617700E-04
Normal-vs-Post-menopause
1.62447832963153E-12
Pre-menopause-vs-Peri-menopause
4.397000E-01
Pre-menopause-vs-Post-menopause
1.792170E-02
Peri-menopause-vs-Post-menopause
7.954400E-01
The Beta value indicates level of DNA methylation ranging from 0 (unmethylated) to 1 (fully methylated). Different beta value cut-off has been considered to indicate hyper-methylation [Beta value: 0.7 - 0.5] or hypo-methylation [Beta-value: 0.3 - 0.25]. PMID: 29027401, 23291739
TP53 mutation status is obtained from TCGA whole exome sequencing data. We downloaded Mutation Annotation Format (MAF) files (derived from VarScan2) from Genomic Data Commons portal. The sample with/without TP53 mutation were matched with RNA-seq data.
PROBES
CLICK TO SEE PROBE LIST. Please note that the Beta value is the ratio of the methylated probe intensity and the sum of methylated and unmethylated probe intensity. Beta value ranges from 0 to 1. The above boxplot represents beta values of CpG probes located upto 1500bp upstream of gene's start site [TSS200, TSS1500]
NOTEa
Whole exome sequencing data is not available for 36 samples.