ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network.
Pathway level understanding of cancer plays a key role in precision oncology. However, the current amount of high-throughput data cannot support the elucidation of full pathway topology. In this study, instead of directly learning the pathway network, we adapted the probabilistic OR gate to model th...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2021-04-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008792&type=printable |
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| author | Lifan Liang Kunju Zhu Junyan Tao Songjian Lu |
| author_facet | Lifan Liang Kunju Zhu Junyan Tao Songjian Lu |
| author_sort | Lifan Liang |
| collection | DOAJ |
| description | Pathway level understanding of cancer plays a key role in precision oncology. However, the current amount of high-throughput data cannot support the elucidation of full pathway topology. In this study, instead of directly learning the pathway network, we adapted the probabilistic OR gate to model the modular structure of pathways and regulon. The resulting model, OR-gate Network (ORN), can simultaneously infer pathway modules of somatic alterations, patient-specific pathway dysregulation status, and downstream regulon. In a trained ORN, the differentially expressed genes (DEGs) in each tumour can be explained by somatic mutations perturbing a pathway module. Furthermore, the ORN handles one of the most important properties of pathway perturbation in tumours, the mutual exclusivity. We have applied the ORN to lower-grade glioma (LGG) samples and liver hepatocellular carcinoma (LIHC) samples in TCGA and breast cancer samples from METABRIC. Both datasets have shown abnormal pathway activities related to immune response and cell cycles. In LGG samples, ORN identified pathway modules closely related to glioma development and revealed two pathways closely related to patient survival. We had similar results with LIHC samples. Additional results from the METABRIC datasets showed that ORN could characterize critical mechanisms of cancer and connect them to less studied somatic mutations (e.g., BAP1, MIR604, MICAL3, and telomere activities), which may generate novel hypothesis for targeted therapy. |
| format | Article |
| id | doaj-art-0cc5c515a0144e62917ca62ff25645ae |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2021-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-0cc5c515a0144e62917ca62ff25645ae2025-08-20T02:01:04ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582021-04-01174e100879210.1371/journal.pcbi.1008792ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network.Lifan LiangKunju ZhuJunyan TaoSongjian LuPathway level understanding of cancer plays a key role in precision oncology. However, the current amount of high-throughput data cannot support the elucidation of full pathway topology. In this study, instead of directly learning the pathway network, we adapted the probabilistic OR gate to model the modular structure of pathways and regulon. The resulting model, OR-gate Network (ORN), can simultaneously infer pathway modules of somatic alterations, patient-specific pathway dysregulation status, and downstream regulon. In a trained ORN, the differentially expressed genes (DEGs) in each tumour can be explained by somatic mutations perturbing a pathway module. Furthermore, the ORN handles one of the most important properties of pathway perturbation in tumours, the mutual exclusivity. We have applied the ORN to lower-grade glioma (LGG) samples and liver hepatocellular carcinoma (LIHC) samples in TCGA and breast cancer samples from METABRIC. Both datasets have shown abnormal pathway activities related to immune response and cell cycles. In LGG samples, ORN identified pathway modules closely related to glioma development and revealed two pathways closely related to patient survival. We had similar results with LIHC samples. Additional results from the METABRIC datasets showed that ORN could characterize critical mechanisms of cancer and connect them to less studied somatic mutations (e.g., BAP1, MIR604, MICAL3, and telomere activities), which may generate novel hypothesis for targeted therapy.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008792&type=printable |
| spellingShingle | Lifan Liang Kunju Zhu Junyan Tao Songjian Lu ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network. PLoS Computational Biology |
| title | ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network. |
| title_full | ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network. |
| title_fullStr | ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network. |
| title_full_unstemmed | ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network. |
| title_short | ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network. |
| title_sort | orn inferring patient specific dysregulation status of pathway modules in cancer with or gate network |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008792&type=printable |
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