Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis
<p>Accurate prediction of cancer prognosis based on gene expression data is generally difficult, and identifying robust prognostic markers for cancer remains a challenging problem. Recent studies have shown that modular markers, such as pathway markers and subnetwork markers, can provide bette...
محفوظ في:
| المؤلف الرئيسي: | |
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| مؤلفون آخرون: | |
| منشور في: |
2014
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| الموضوعات: | |
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إضافة وسم
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| _version_ | 1864513506582200320 |
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| author | Navadon Khunlertgit (3480926) |
| author2 | Byung-Jun Yoon (142313) |
| author2_role | author |
| author_facet | Navadon Khunlertgit (3480926) Byung-Jun Yoon (142313) |
| author_role | author |
| dc.creator.none.fl_str_mv | Navadon Khunlertgit (3480926) Byung-Jun Yoon (142313) |
| dc.date.none.fl_str_mv | 2014-11-06T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1186/s13637-014-0019-9 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Simultaneous_identification_of_robust_synergistic_subnetwork_markers_for_effective_cancer_prognosis/26869906 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Bioinformatics and computational biology Biomedical and clinical sciences Oncology and carcinogenesis Cancer classification Subnetwork marker identification Protein-protein interaction network Message-passing algorithm |
| dc.title.none.fl_str_mv | Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p>Accurate prediction of cancer prognosis based on gene expression data is generally difficult, and identifying robust prognostic markers for cancer remains a challenging problem. Recent studies have shown that modular markers, such as pathway markers and subnetwork markers, can provide better snapshots of the underlying biological mechanisms by incorporating additional biological information, thereby leading to more accurate cancer classification. In this paper, we propose a novel method for simultaneously identifying robust synergistic subnetwork markers that can accurately predict cancer prognosis. The proposed method utilizes an efficient message-passing algorithm called affinity propagation, based on which we identify groups – or subnetworks – of discriminative and synergistic genes, whose protein products are closely located in the protein-protein interaction (PPI) network. Unlike other existing subnetwork marker identification methods, our proposed method can simultaneously identify multiple nonoverlapping subnetwork markers that can synergistically predict cancer prognosis. Evaluation results based on multiple breast cancer datasets demonstrate that the proposed message-passing approach can identify robust subnetwork markers in the human PPI network, which have higher discriminative power and better reproducibility compared to those identified by previous methods. The identified subnetwork makers can lead to better cancer classifiers with improved overall performance and consistency across independent cancer datasets.</p><h2>Other Information</h2> <p> Published in: EURASIP Journal on Bioinformatics and Systems Biology<br> License: <a href="http://creativecommons.org/licenses/by/4.0" target="_blank">http://creativecommons.org/licenses/by/4.0</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1186/s13637-014-0019-9" target="_blank">https://dx.doi.org/10.1186/s13637-014-0019-9</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_11b956383c75efb8fe5e1c07b7424d07 |
| identifier_str_mv | 10.1186/s13637-014-0019-9 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/26869906 |
| publishDate | 2014 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosisNavadon Khunlertgit (3480926)Byung-Jun Yoon (142313)Biological sciencesBioinformatics and computational biologyBiomedical and clinical sciencesOncology and carcinogenesisCancer classificationSubnetwork marker identificationProtein-protein interaction networkMessage-passing algorithm<p>Accurate prediction of cancer prognosis based on gene expression data is generally difficult, and identifying robust prognostic markers for cancer remains a challenging problem. Recent studies have shown that modular markers, such as pathway markers and subnetwork markers, can provide better snapshots of the underlying biological mechanisms by incorporating additional biological information, thereby leading to more accurate cancer classification. In this paper, we propose a novel method for simultaneously identifying robust synergistic subnetwork markers that can accurately predict cancer prognosis. The proposed method utilizes an efficient message-passing algorithm called affinity propagation, based on which we identify groups – or subnetworks – of discriminative and synergistic genes, whose protein products are closely located in the protein-protein interaction (PPI) network. Unlike other existing subnetwork marker identification methods, our proposed method can simultaneously identify multiple nonoverlapping subnetwork markers that can synergistically predict cancer prognosis. Evaluation results based on multiple breast cancer datasets demonstrate that the proposed message-passing approach can identify robust subnetwork markers in the human PPI network, which have higher discriminative power and better reproducibility compared to those identified by previous methods. The identified subnetwork makers can lead to better cancer classifiers with improved overall performance and consistency across independent cancer datasets.</p><h2>Other Information</h2> <p> Published in: EURASIP Journal on Bioinformatics and Systems Biology<br> License: <a href="http://creativecommons.org/licenses/by/4.0" target="_blank">http://creativecommons.org/licenses/by/4.0</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1186/s13637-014-0019-9" target="_blank">https://dx.doi.org/10.1186/s13637-014-0019-9</a></p>2014-11-06T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1186/s13637-014-0019-9https://figshare.com/articles/journal_contribution/Simultaneous_identification_of_robust_synergistic_subnetwork_markers_for_effective_cancer_prognosis/26869906CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/268699062014-11-06T03:00:00Z |
| spellingShingle | Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis Navadon Khunlertgit (3480926) Biological sciences Bioinformatics and computational biology Biomedical and clinical sciences Oncology and carcinogenesis Cancer classification Subnetwork marker identification Protein-protein interaction network Message-passing algorithm |
| status_str | publishedVersion |
| title | Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis |
| title_full | Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis |
| title_fullStr | Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis |
| title_full_unstemmed | Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis |
| title_short | Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis |
| title_sort | Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis |
| topic | Biological sciences Bioinformatics and computational biology Biomedical and clinical sciences Oncology and carcinogenesis Cancer classification Subnetwork marker identification Protein-protein interaction network Message-passing algorithm |