The role of general epigenetic mechanisms in carcinogenesis and tumor aggressiveness is well documented: CpG island hyper-methylation silences tumor suppressor genes, whereas hypo-methylation promotes the transcriptional activation of oncogenes and induces chromosomal instability. This pipeline calculates and identifies correlations between DNA methylation and gene expression profiles using the available array technologies.
The top 25 correlated methylation probe(s) per gene are displayed. Total number of matched samples = 313 Number of gene expression samples = 315 Number of methylation samples = 529
Figure 1. Histogram of methylation correlation values. n is the number of matched samples between Level 3 CpG site methylation and Level 3 gene expression arrays. Number of Matched Samples = 313
Figure 2. Plot 1. The estimated pi_0 versus the tuning parameter lambda. Plot 2. The q-values versus the p-values Plot 3. The number of significant tests versus each q-value cutoff Plot 4. The number of expected false positives versus the number of significant tests. The first is a plot of the estimate of pi_0 versus its tuning parameter lambda. In most cases, as lambda gets larger, the bias of the estimate decreases, yet the variance increases. Comparing your estimate of pi_0 to this plot allows one to guage its quality. The remaining three plots show how many tests are significant, as well as how many false positives to expect for each q-value cut-off.
Table 1. Get Full Table Top 25 most negatively correlated methylation probe(s) per gene. Correlation Coefficient: See Methods & Data below. Expression Mean and Expression Variance: median and variance of gene expression levels of gene expression probes associated with the gene. Methylation Mean and Methylation Variance: median and variance of methylation levels of CpG methylation probes associated with the gene.
| Meth_Probe | Gene | Chrom | Position | Corr_Spearman | Pval_Spearman | Qval | Expr_Mean | Meth_Mean |
|---|---|---|---|---|---|---|---|---|
| cg15518883 | SIT1 | 9 | 35640561 | -0.86 | 0 | 0 | -7.705e-01 | 0.79928 |
| cg24674703 | CD5 | 11 | 60626536 | -0.86 | 0 | 0 | -5.636e-01 | 0.81197 |
| cg05740244 | LDHC | 11 | 18390591 | -0.81 | 0 | 0 | -3.678e-01 | NA |
| cg10045881 | CHI3L2 | 1 | 111571814 | -0.77 | 0 | 0 | 1.188e-02 | 0.47701 |
| cg11584936 | BNIPL | 1 | 149276212 | -0.76 | 0 | 0 | 1.938e+00 | 0.31498 |
| cg07347645 | SYCP2 | 20 | 57940566 | -0.75 | 0 | 0 | 4.857e-01 | 0.49777 |
| cg00083937 | MAPK8IP2 | 22 | 49386671 | -0.75 | 0 | 0 | 1.164e+00 | 0.50124 |
| cg20792833 | PTPRCAP | 11 | 66961771 | -0.75 | 0 | 0 | 6.558e-04 | 0.74735 |
| cg24392574 | CALML5 | 10 | 5531423 | -0.75 | 0 | 0 | 5.981e-01 | 0.85287 |
| cg11600161 | TBC1D10C | 11 | 66928161 | -0.75 | 0 | 0 | -6.352e-01 | 0.74207 |
| cg09886641 | SPESP1 | 15 | 67010072 | -0.75 | 0 | 0 | -5.392e-01 | 0.72197 |
| cg22214414 | SYCP2 | 20 | 57940627 | -0.74 | 0 | 0 | 4.857e-01 | 0.54212 |
| cg03534410 | TMEM40 | 3 | 12776112 | -0.74 | 0 | 0 | 9.764e-01 | 0.58588 |
| cg16363586 | BST2 | 19 | 17377329 | -0.74 | 0 | 0 | 2.395e-01 | 0.38680 |
| cg18738906 | SCNN1A | 12 | 6354000 | -0.74 | 0 | 0 | 1.564e+00 | 0.66035 |
| cg22266967 | S100P | 4 | 6746599 | -0.74 | 0 | 0 | -8.515e-01 | 0.53894 |
| cg24841244 | CD3D | 11 | 117718540 | -0.73 | 0 | 0 | -2.799e+00 | 0.75201 |
| cg09522147 | KRT7 | 12 | 50913609 | -0.73 | 0 | 0 | 1.689e+00 | 0.41206 |
| cg17078393 | LCK | 1 | 32489589 | -0.73 | 0 | 0 | -1.960e+00 | 0.77617 |
| cg09902130 | CD6 | 11 | 60495754 | -0.73 | 0 | 0 | 1.199e-01 | 0.81638 |
| cg00328227 | C1orf59 | 1 | 109005848 | -0.72 | 0 | 0 | -3.380e-01 | 0.37292 |
| cg13840968 | CIDEB | 14 | 23850766 | -0.72 | 0 | 0 | 5.331e-02 | 0.59608 |
| cg07621046 | C10orf82 | 10 | 118419648 | -0.72 | 0 | 0 | 1.105e-01 | 0.53250 |
| cg24926276 | LRG1 | 19 | 4490943 | -0.72 | 0 | 0 | 6.687e-01 | 0.37548 |
| cg05982504 | IGFALS | 16 | 1784963 | -0.72 | 0 | 0 | 1.535e+00 | 0.53917 |
| cg23207527 | RBM24 | 6 | 17391092 | -0.71 | 0 | 0 | 1.005e-01 | 0.63109 |
Methylation Array Platforms: Illumina Infinium HumanMethylation27, Illumina DNA Methylation OMA002, Illumina DNA Methylation OMA003
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methylation file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA/1668809/2.GDAC_MergeDataFiles.Finished/BRCA.methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.data.txt
Gene Expression Platforms: Agilent 244K Gene Expression G4502A-07-1, Agilent 244K Gene Expression G4502A-07-2, Agilent 244K Gene Expression G4502A-07-3, Affymetrix Human Exon 1.0 ST Array, Affymetrix HT Human Genome U133 Array
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gene expression file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/BRCA/1676448/0.GDAC_mRNA_Preprocess_Median.Finished/BRCA.medianexp.txt
Level 3 methylation and gene expression arrays were paired on the basis of Entrez Gene ID concordance. The association between CpG site methylation and the level of expression of the corresponding genes was determined by calculating a correlation measure between the two platforms
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correlation measure = Spearman