The same TCGA sample is profiled to detect the copy number variations and expressions of genes. This pipeline tries to correlate the copy number and expression data of genes across samples to if the copy number variations of genes also result in differential expressions

This page contains the calculated correlation coefficients based on measurements of genomic copy number (log2) values and intensitiy of the expressions of the the corresponding feature across patients. High positive/low negative correlation coefficients indicate that genomic alterations result in differences in the expressions of the features (microRNA or mRAN) the genomic regions transcribe.

Number of genes and samples used for the calculation are shown in Table 1. Figure 1 shows the distribution of calculated correlation coefficients and quantile-quantile plot of the calculated correlation coefficients against a normal distribution. Table 2 shows the top 20 features ordered by the value of correltion coefficients.

Category | Copy number | Expression | Common |

Sample | 56 | 33 | 21 |

Genes | 29390 | 17815 | 15551 |

Hybridization.REF | cor | p | q | chrom | start | end | geneid |

MRPL51 | 0.9581 | 8.97459884185992e-12 | 7.1649771478688e-08 | 12 | 6471577 | 6472718 | 51258 |

C14orf166 | 0.9546 | 1.92592608527775e-11 | 7.68792936188762e-08 | 14 | 51525943 | 51541163 | 51637 |

PSMC6 | 0.939 | 2.96587199244414e-10 | 7.89279663036257e-07 | 14 | 52243668 | 52264466 | 5706 |

ORAOV1 | 0.9301 | 1.04556230340336e-09 | 1.71044373810287e-06 | 11 | 69189512 | 69199346 | 220064 |

POP4 | 0.9299 | 1.07122088977007e-09 | 1.71044373810287e-06 | 19 | 34789041 | 34798547 | 10775 |

SCFD1 | 0.9276 | 1.45482514923856e-09 | 1.93579477889302e-06 | 14 | 30161272 | 30274769 | 23256 |

PIK3C3 | 0.9228 | 2.60701860099743e-09 | 2.97334877013278e-06 | 18 | 37789197 | 37915446 | 5289 |

POLR2F | 0.9211 | 3.20894177896491e-09 | 3.20237078562836e-06 | 22 | 36679664 | 36693752 | 5435 |

MRPL21 | 0.9151 | 6.26991769614449e-09 | 4.63604728189718e-06 | 11 | 68415322 | 68427879 | 219927 |

PSMA6 | 0.9149 | 6.38764507954193e-09 | 4.63604728189718e-06 | 14 | 34831325 | 34856431 | 5687 |

UQCRFS1 | 0.9149 | 6.38487462900628e-09 | 4.63604728189718e-06 | 19 | 34390007 | 34395954 | 7386 |

TBL2 | 0.9132 | 7.69075980677769e-09 | 5.08673693909369e-06 | 7 | 72621935 | 72630908 | 26608 |

SEC61A1 | 0.9118 | 8.92005536101692e-09 | 5.08673693909369e-06 | 3 | 129253902 | 129273216 | 29927 |

VPS41 | 0.9118 | 8.90783380391724e-09 | 5.08673693909369e-06 | 7 | 38730068 | 38915325 | 27072 |

LSG1 | 0.9108 | 9.82679893013483e-09 | 5.23022744613477e-06 | 3 | 195842812 | 195874200 | 55341 |

FGFR1OP2 | 0.9086 | 1.23130021734141e-08 | 6.07653079184533e-06 | 12 | 26982583 | 27010129 | 26127 |

MRPL46 | 0.9081 | 1.29391235503817e-08 | 6.07653079184533e-06 | 15 | 86803714 | 86811623 | 26589 |

C18orf21 | 0.9004 | 2.68662936342423e-08 | 1.19161240722739e-05 | 18 | 31806586 | 31813239 | 83608 |

UBL7 | 0.8986 | 3.17753503509266e-08 | 1.26122292394471e-05 | 15 | 72525371 | 72540582 | 84993 |

KLHL11 | 0.8985 | 3.19446820107316e-08 | 1.26122292394471e-05 | 17 | 37263325 | 37275155 | 55175 |

Level III gene level expression data and gene by sample copy number data derived by using the CNTools package of Bioconductor were used for the calculations. Pearson correlation coefficients were calculated for each pair of genes shared by the two data sets across all the samples that were common.

Pairwise correlations between the log2 copy numbers and expressions of each gene across samples were calculated using Pearson correlation.