Table 2.
OncoCis annotations of mutations from 17 whole breast cancer genomes sorted by differential gene expression P -value of the sample where there is an associated mutation and the samples without any associated mutation for a particular gene
| Distance | Gene expression | Conservation | Motifs | Fantom5 | RegulomeDB | Funseq | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chromosome | Position | Sample ID | Gene | to TSS | Fold change | P -value | DHS | H3K4me1 | H3K4me3 | H3K27ac | Mutated base | Created | Removed | Promoter | Enhancer | Category | Sensitive? |
| Chr6 | 71,108,774 | PD4006a | COL9A1 | -95,988 | 100.12 | 1.39E-23 | 1 | 1 | 1 | 1 | 1 | Hand1::Tcfe2a | Klf1 | 1 | 0 | 4 | No |
| Chr1 | 160,094,923 | PD4116a | ATP1A2 | -9,404 | 71.15 | 2.99E-19 | 1 | 1 | 0 | 1 | 0.981 | ELF1;Hltf | SP1;ZEB1 | 1 | 0 | 4 | No |
| Chr7 | 92,347,495 | PD4107a | CDK6 | 118,446 | 5.06 | 7.75E-07 | 1 | 1 | 1 | 1 | 1 | - | NFIC;THAP1 | 1 | 0 | 4 | No |
| Chr9 | 109,651,512 | PD4006a | ZNF462 | -26,135 | 4.79 | 2.27E-06 | 1 | 1 | 0 | 1 | 0.993 | - | EHF;Erg;FLI1;PPARG::RXRA;. | 0 | 0 | 5 | No |
| Chr1 | 208,412,585 | PD4116a | PLXNA2 | 5,080 | 1.63 | 4.17E-06 | 1 | 1 | 0 | 1 | 0.993 | Nobox;Hltf | - | 0 | 1 | 4 | No |
| Chr4 | 7,5560,994 | PD4103a | BTC | 158,888 | 2.38 | 7.39E-05 | 1 | 1 | 0 | 0 | 0.938 | - | CREB1;Mafb | 0 | 0 | 4 | No |
| Chr5 | 97,643,723 | PD4109a | RGMB | 461,275 | 2.50 | 2.47E-04 | 1 | 1 | 0 | 1 | 0.801 | - | ARID3A | 0 | 1 | 3a | No |
| Chr17 | 2,080,270 | PD4005a | HIC1 | -120,667 | 1.29 | 4.02E-04 | 1 | 1 | 0 | 1 | 1 | NFIC | - | 0 | 0 | 5 | No |
| Chr16 | 57,334,425 | PD4115a | PLLP | -15,841 | 2.09 | 8.51E-04 | 1 | 1 | 1 | 1 | 1 | - | TFAP2C | 1 | 0 | 4 | Yes |
| Chr2 | 219,147,431 | PD4198a | TMBIM1 | 9,849 | 1.65 | 2.23E-03 | 1 | 1 | 0 | 1 | 0.973 | Foxd3 | NFATC2;Erg | 1 | 0 | 5 | No |
| Chr8 | 100,811,550 | PD4116a | COX6C | 94,692 | 2.46 | 2.63E-03 | 1 | 1 | 0 | 0 | 1 | - | NFKB1;Stat4;Spi1;Bcl6 | 0 | 0 | 2b | No |
| Chr14 | 37,612,228 | PD4115a | SLC25A21 | 29,637 | 1.54 | 3.15E-03 | 1 | 1 | 0 | 0 | 1 | Hand1::Tcfe2a | RUNX1;RUNX2;FOXI1 | 0 | 0 | 2b | No |
| Chr1 | 185,688,035 | PD4005a | HMCN1 | 15,647 | 0.61 | 4.98E-03 | 1 | 1 | 0 | 1 | 0.997 | FOXP1;FOXL1 | - | 0 | 0 | 5 | No |
| Chr2 | 208,890,286 | PD3904a | PLEKHM3 | -2 | 1.48 | 1.09E-02 | 1 | 1 | 1 | 1 | 0.998 | - | ELF5;GABPA;FLI1;ELK4;ELK1 | 1 | 0 | 2b | No |
| Chr10 | 93,058,182 | PD4005a | PCGF5 | -77,814 | 0.65 | 2.28E-02 | 1 | 1 | 0 | 0 | 0.935 | - | Zfx | 1 | 0 | 2a | No |
| Chr7 | 22,617,382 | PD4107a | IL6 | -149,383 | 2.29 | 2.62E-02 | 1 | 1 | 0 | 1 | 1 | Hltf;CEBPA;CEBPB | AR | 1 | 1 | 2a | Yes |
| Chr6 | 26,533,145 | PD4192a | HMGN4 | 5,426 | 0.49 | 2.62E-02 | 1 | 1 | 0 | 0 | 0.979 | - | Zfx | 0 | 1 | 2b | Yes |
| Chr22 | 31,644,327 | PD4103a | LIMK2 | -36,078 | 0.79 | 3.43E-02 | 1 | 1 | 1 | 1 | 0.989 | - | Klf4;SP2;SP1;KLF5;Klf1;ELK1 | 1 | 0 | 3a | No |
All mutations in the list are selected based on having a DHS, either a H3K4me1 or H3K4me3 histone mark, conservation (phastCons) >0.8 and the creation or removal of at least one transcription factor binding motif. The category and whether the mutation falls within a ‘sensitive’ region as defined by RegulomeDB and Funseq, respectively, are also shown.