Table 2.
Application of proMODMatcher to mRNA and RPPA profiles of TCGA BRCA data
| Data type Type 1 | Type 2 | No. samples1 | No. cis pair2 | No. (%) self-aligned | No. of cross | Cross-aligned pairs Type 1 | Self-aligned in RNA-CNV3 | Cross-aligned pairs Type 2 | By MODMatcher4 |
|---|---|---|---|---|---|---|---|---|---|
| RNAseq | RPPA | 856 | 104/151 | 687 (80.3) | 1 | TCGA-A7-A56D-01 | Y | TCGA-W8-A86G-01 | Y |
| Agilent | RPPA | 424 | 97/145 | 360 (84.9) | 11 | TCGA-BH-A0DS-01 | No: TCGA-BH-A0BA-01 | TCGA-E2-A1IL-01 | Y |
| TCGA-E2-A10C-01 | Y | TCGA-LL-A5YN-01 | Y | ||||||
| TCGA-E2-A1B0-01 | Y | TCGA-D8-A1JK-01 | Y | ||||||
| TCGA-AR-A1AV-01 | No: TCGA-AR-A1AW-01 | TCGA-AR-A1AW-01 | No | ||||||
| TCGA-E2-A1B6-01 | No: TCGA-E2-A1B5-01 | TCGA-AR-A255-01 | No | ||||||
| TCGA-A8-A07J-01 | Y | TCGA-D8-A1JU-01 | No | ||||||
| TCGA-A8-A0AB-01 | Y | TCGA-EW-A1J3-01 | No | ||||||
| TCGA-AN-A04C-01 | Y | TCGA-E9-A1N9-01 | No | ||||||
| TCGA-E2-A105-01 | Y | TCGA-C8-A1HO-01 | Y | ||||||
| TCGA-AN-A0XL-01 | Y | TCGA-D8-A1Y2-01 | No | ||||||
| TCGA-AN-A0XV-01 | Y | TCGA-GM-A2DM-01 | No |
The boldface indicates cross-alignments supported by other data.
1The number of common sample with both Type 1 and Type 2 profiles.
2The number of significant cis-pairs at q-value < 0.05 at final iteration and the number of cis-pairs investigated.
3Indicates whether the RNA sample of cross-aligned pairs are self-aligned in alignment between RNA profile (Agilent array or RNAseq) and CNV profile. The aligned pairs are also shown if there is a cross-aligned sample.
4Indicates that cross-aligned pairs are cross-aligned by MODMatcher.