Patient-Specific Network for Personalized Breast Cancer Therapy with Multi-Omics Data
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data
2.2. Survival Analysis
2.3. Protein-Protein Interaction
3. Results
3.1. Proposed Approach
3.2. Step 1: Survival Analysis
3.3. Step 2: Copy Number Analysis
3.4. Step 3: Protein-Protein Interaction Analysis
3.5. Step 4: Drug-Protein Interaction Analysis
3.6. Validation
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Proteins | Frequency | Drugs |
---|---|---|
BRCA1, TP53 | 40 | cyclophosphamide or doxorubicin or gemcitabine or olaparib or paclitaxel or tamoxifen (BRCA1 and TP53) |
TP53 | 7 | Gemcitabine or epirubicin or doxorubicin or paclitaxel or capecitabine or docetaxel or thiotepa or abemaciclib or tamoxifen or olaparib or cyclophosphamide or alpelisib (TP53) |
PSMD4 | 6 | Talazoparib |
BRCA1, PSMD4 | 3 | talazoparib (BRCA1 and PSMD4) |
BRCA1, HDAC2, TP53 | 2 | olaparib (BRCA1, HDAC2 and TP53) |
BRCA1, PSMD4, TP53 | 2 | talazoparib (BRCA1 and PSMD4) and gemcitabine or epirubicin or doxorubicin or paclitaxel or capcitabine or docetaxel or thiotepa or abemaciclib or tamoxifen or olaparib or cyclophosphamide or alpelisib (TP53) |
PSMD4, RB1 | 2 | talazoparib (PSMD4) and fulvestrant or palbociclib or methotrexate or ribociclib or everolimus (RB1) |
BRCA1 | 1 | doxorubicin or cyclophosphamide or talazoparib or olaparib or gemcitabine or tamoxifen or paclitaxel or everolimus (BRCA1) |
BRCA1, PIK3R1 | 1 | doxorubicin or cyclophosphamide or talazoparib or olaparib or gemcitabine or tamoxifen or paclitaxel or everolimus (BRCA1) and alpelisib (PIK3R1) |
BRCA1, PIK3R1, PSMD4, TP53 | 1 | talazoparib (BRCA1 and PSMD4) and alpelisib (PIK3R1 and TP53) |
BRCA1, PIK3R1, TP53 | 1 | cyclophosphamide or doxorubicin or gemcitabine or olaparib or paclitaxel or tamoxifen (BRCA and TP53) and alpelisib (PIK3R1) |
BRCA1, RB1 | 1 | everolimus (BRCA1 and RB1) |
HDAC2 | 1 | olaparib (HDAC2) |
HDAC2 PIK3R1 TP53 | 1 | olaparib (HDAC2 and TP53) alpelisib (PIK3R1) |
MCL1 | 1 | docetaxel (MCL1) |
PSMD4, TP53 | 1 | talazoparib (PSMD4) and gemcitabine or epirubicin or doxorubicin or paclitaxel or capecitabine or docetaxel or thiotepa or abemaciclib or tamoxifen or olaparib or cyclophosphamide or alpelisib (TP53) |
RB1 | 1 | fulvestrant or palbociclib or methotrexate or ribociclib or everolimus |
RB1, TP53 | 1 | fulvestrant or palbociclib or methotrexate or ribociclib or everolimus (RB1) and gemcitabine or epirubicin or doxorubicin or paclitaxel or capecitabine or docetaxel or thiotepa or abemaciclib or tamoxifen or olaparib or cyclophosphamide or alpelisib (TP53) |
Proteins | Frequency | Drugs |
---|---|---|
BRCA1 TP53 | 2 | cyclophosphamide or doxorubicin or gemcitabine or olaparib or paclitaxel or tamoxifen (BRCA1 and TP53) |
BRCA1 HDAC2 | 2 | olaparib (BRCA1 and HDAC2) |
BRCA1 PSMD4 | 2 | talazoparib (BRCA1 and PSMD4) |
BRCA1 RB1 TP53 | 1 | cyclophosphamide or doxorubicin or gemcitabine or olaparib or paclitaxel or tamoxifen (BRCA1 and TP53) and fulvestrant or palbociclib or methotrexate or ribociclib or everolimus (RB1) |
HDAC2 PIK3R1 PSMD4 | 1 | olaparib (HDAC2) alpelisib (PIK3R1) talazoparib (PSMD4) |
Proteins | Frequency | Drugs |
---|---|---|
BRCA1 TP53 | 6 | cyclophosphamide or doxorubicin or gemcitabine or olaparib or paclitaxel or tamoxifen (BRCA1 and TP53) |
BRCA1 PSMD4 | 3 | talazoparib (BRCA1 and PSMD4) |
BRCA1 | 2 | doxorubicin or cyclophosphamide or talazoparib or olaparib or gemcitabine or tamoxifen or paclitaxel or everolimus (BRCA1) |
TP53 | 2 | Gemcitabine or epirubicin or doxorubicin or paclitaxel or capecitabine or docetaxel or thiotepa or abemaciclib or tamoxifen or olaparib or cyclophosphamide or alpelisib (TP53) |
ACTB PSMD4 TP53 | 1 | Cyclophosphamide (ACTB and TP53) and talazoparib (PSMD4) |
BRCA1 PSMD4 RB1 TP53 | 1 | cyclophosphamide or doxorubicin or gemcitabine or olaparib or paclitaxel or tamoxifen (BRCA1 and TP53) and Talazoparib (PSMD4) and Gemcitabine or epirubicin or doxorubicin or paclitaxel or capecitabine or docetaxel or thiotepa or abemaciclib or tamoxifen or olaparib or cyclophosphamide or alpelisib (TP53) |
PIK3R1 | 1 | Alpelisib |
PSMD4 TP53 | 1 | talazoparib (PSMD4) and gemcitabine or epirubicin or doxorubicin or paclitaxel or capecitabine or docetaxel or thiotepa or abemaciclib or tamoxifen or olaparib or cyclophosphamide or alpelisib (TP53) |
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Cava, C.; Sabetian, S.; Castiglioni, I. Patient-Specific Network for Personalized Breast Cancer Therapy with Multi-Omics Data. Entropy 2021, 23, 225. https://doi.org/10.3390/e23020225
Cava C, Sabetian S, Castiglioni I. Patient-Specific Network for Personalized Breast Cancer Therapy with Multi-Omics Data. Entropy. 2021; 23(2):225. https://doi.org/10.3390/e23020225
Chicago/Turabian StyleCava, Claudia, Soudabeh Sabetian, and Isabella Castiglioni. 2021. "Patient-Specific Network for Personalized Breast Cancer Therapy with Multi-Omics Data" Entropy 23, no. 2: 225. https://doi.org/10.3390/e23020225