| Perturbation type | Gene | Citation | Cancer type | Gene-disease relation |
|---|---|---|---|---|
| Top gains | CDC25C | 22871320 | BRCA | The modulation of CDC25C alternative splicing as an additional regulatory event involved in cellular response to DNA damage in breast cancer cells. |
| Top gains | TDO2 | 26363006 | Triple-negative BRCA | In vivo: TDO2 inhibitor-treated TNBC cells inhibited colonization of the lung: suggesting that TDO2 enhanced metastatic capacity. |
| Top cancer-specific gains | UPF2 | 24489661 | BRCA | The overexpression of UPF2 (10p14) was associated with basal breast cancer. |
| Top cancer-specific gains | HS3ST3A1 | 27041583 | BRCA | The heparan sulfate sulfotransferase 3-OST3A (HS3ST3A) is a novel tumor regulator and a prognostic marker in breast cancer. |
| Top losses | ALK | 26384210 | Aggressive BRCA | ALK is overexpressed in a substantial proportion of breast cancers and possibly plays a significant role in the aggressive behavior of this cancer. |
| Top losses | APOB | 26804063 | BRCA | Female breast cancer risk was inversely associated with ApoB. |
| Top losses | APP | 27980417 | BRCA | Patients with tumors with higher TARBP2 or APP expression had unfavorable prognoses. |
| Top losses | ASB14 | 21586611 | BRCA | Up-regulated in breast tumor tissues. |
| Top losses | AURKC | 25994570 | BRCA | Breast tumors showed significant overexpression of AURKC in comparison to normal breast tissues. |
| Top losses | AVPR2 | 21586611 | BRCA | Down-regulated in breast tumor tissues. |
| Top losses | C1QTNF9 | 17389037 | BRCA | Differentially expressed in invasive ductal and lobular carcinomas compared to normal samples. |
| Top losses | CCDC36 | 28179314 | BRCA | CCDC36 (42.7 vs. 16.2%) showed significantly higher methylation in breast tumor compared to adjacent non-tumor tissues. |
| Top losses | DMRT3 | 17389037 | BRCA | Differentially expressed in invasive ductal and lobular carcinomas compared to normal samples. |
| Top losses | ENPP6 | 17389037 | BRCA | Differentially expressed in invasive ductal and lobular carcinomas compared to normal samples. |
| Top losses | ESR2 | 29414691 | BRCA | ESR2 gene variants assciated with the a risk of breast cancer. |
| Top losses | GFAP | 25663547 | BRCA | GFAP were among the genes overexpressed in resistant breast cancer luminal cell lines. |
| Top losses | HOXD4 | 19232136 | BRCA | HOX4 is overexpressed in canine mammary tumor cell lines CMT12:CMT27: CMT28 from spontaneous tumors. |
| Top losses | HRNR | 22727333 | BRCA | HRNR expression is decreased in invasive ductal carcinomas compared to invasive lobular carcinomas and less aggressive breast carcinoma phenotypes: and cellular expression of hornerin is altered during induction of apoptosis. |
| Top losses | INCA1 | 21532620 | Triple-negative BRCA | Differentially expressed in triple negative carcinomas compared to non-triple negative samples. |
| Top losses | KCNA5 | 30250548 | BRCA | KCNA5 is associated with the survival of malignant tumors: including breast cancer. |
| Top losses | LURAP1 | 17389037 | BRCA | Differentially expressed in invasive ductal and lobular carcinomas compared to normal samples. |
| Top losses | MAP1LC3C | 27256984 | BRCA | MAP1LC3C was also frequently amplified in breast cancer. |
| Top losses | MASP1 | 17389037 | BRCA | Differentially expressed in invasive ductal and lobular carcinomas compared to normal samples. |
| Top losses | MYH7B | 17389037 | BRCA | Differentially expressed in invasive ductal and lobular carcinomas compared to normal samples. |
| Top losses | MYOC | 17389037 | BRCA | Differentially expressed in invasive ductal and lobular carcinomas compared to normal samples. |
| Top losses | MYOCD | Cell Signal - 2014 26:1335-46. | BRCA | Maspin is transcriptionally induced by MYOCD and the upregulation of Maspin leads to apoptosis of breast cancer cells. |
| Top losses | NOS2 | 29087320 | BRCA | Coexpression of NOS2 and COX2 accelerates tumor growth and reduces survival in estrogen receptor-negative breast cancer. |
| Top losses | PPP2R2B | 20669227 | BRCA | A variant of the rs319217 (PPP2R2B) SNP is a marker of better prognosis in breast cancer. |
| Top losses | USP44 | 26232424 | BRCA | USP44+ cancer stem cell subclones contribute to breast cancer aggressiveness by promoting vasculogenic mimicry. |
| Top cancer-specific losses | FOXF1 | 20587515 | BRCA | FOXF1 as a potential tumor suppressor gene that is epigenetically silenced in breast cancer. |
| SMGs within edgetic gains or losses | AKT1 | 18676830 | BRCA | AKT1 mutations were exclusively observed in brast cancer tumors expressing both ER and progesterone receptor. |
| SMGs within edgetic gains or losses | BAP1 | 26419610 | BRCA | BAP1 promotes breast cancer cell proliferation and metastasis by deubiquitinating KLF5. |
| SMGs within edgetic gains or losses | BRCA1 | 25329591 | BRCA | BRCA1 is a tumor suppressor involved in basic cellular functions necessary for cell replication and DNA synthesis: but reduced expression of BRCA1: due to mutations or epigenetic inactivation: leads to impaired mammary gland differentiation and increased risk of breast cancer development. |
| SMGs within edgetic gains or losses | EP300 | 28341962 | BRCA | EP300 plays a major role in the reprogramming events: leading to a more malignant phenotype with the acquisition of drug resistance and cell plasticity: a characteristic of metaplastic breast cancer. |
| SMGs within edgetic gains or losses | ESR1 | 29414691 | BRCA | ESR2 gene variants with the risk of breast cancer. |
| SMGs within edgetic gains or losses | FBLN2 | 20205715 | BRCA | FBLN2 is methylated in breast cancer cell lines. |
| SMGs within edgetic gains or losses | FOXA1 | 27524420 | BRCA | Twist1 promotes breast cancer invasion and metastasis by silencing Foxa1 expression. |
| SMGs within edgetic gains or losses | KRAS | 28843257 | BRCA | The mutations in BRAF and KRAS genes in breast cancer cells do lower the responsiveness of Trastuzumab drug treatments. |
| SMGs within edgetic gains or losses | MAP3K1 | 28178648 | BRCA | Polymorphisms of ESR1: UGT1A1: HCN1: MAP3K1 and CYP2B6 are associated with the prognosis of hormone receptor-positive early breast cancer. |
| SMGs within edgetic gains or losses | NCOR1 | 27499907 | BRCA | NCOR1 mRNA is an independent prognostic factor for breast cancer. |
| SMGs within edgetic gains or losses | NTRK3 | 12450787:12450792 | BRCA | ETV6-NTRK3 fusion gene in 12(92%) of 13 secretory breast carcino-mas: but only 1 (2%) of 50 infiltratingductal carcinomas |
| SMGs within edgetic gains or losses | PIK3R1 | 24229379 | BRCA | PIK3R1 underexpression is an independent prognostic marker in breast cancer. |
| SMGs within edgetic gains or losses | SALL4 | 27444278 | BRCA | SALL4 expression is commonly upregulated in human breast tumors (~86 %) and that overregulation of this gene is often linked to tumor progression. |
| Top gains | DST (Isoform switch) | 22751464 | Breast cancer | Differentially expressed in ductal carcinoma in situ to invasive breast cancer |
| Top gains | CALM1 (CALM) (Isoform switch) | 18587642 | Breast cancer cell lines | Calmodulin modulates Akt activity in human breast cancer cell lines |
| Top losses | F8 (Isoform switch) | Int Surg J.; 2018; 5;1394-1398 | Breast cancer | Factor VIII levels correlated advancing stage of breast cancer; number of pathological axillary lymph node involved |
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