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Classifying tumors by supervised network propagation
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| Zeitschriftentitel: | Bioinformatics |
|---|---|
| Personen und Körperschaften: | , , |
| In: | Bioinformatics, 34, 2018, 13, S. i484-i493 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Oxford University Press (OUP)
|
| Schlagwörter: |
| author_facet |
Zhang, Wei Ma, Jianzhu Ideker, Trey Zhang, Wei Ma, Jianzhu Ideker, Trey |
|---|---|
| author |
Zhang, Wei Ma, Jianzhu Ideker, Trey |
| spellingShingle |
Zhang, Wei Ma, Jianzhu Ideker, Trey Bioinformatics Classifying tumors by supervised network propagation Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| author_sort |
zhang, wei |
| spelling |
Zhang, Wei Ma, Jianzhu Ideker, Trey 1367-4803 1367-4811 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/bty247 <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Motivation</jats:title> <jats:p>Network propagation has been widely used to aggregate and amplify the effects of tumor mutations using knowledge of molecular interaction networks. However, propagating mutations through interactions irrelevant to cancer leads to erosion of pathway signals and complicates the identification of cancer subtypes.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>To address this problem we introduce a propagation algorithm, Network-Based Supervised Stratification (NBS2), which learns the mutated subnetworks underlying tumor subtypes using a supervised approach. Given an annotated molecular network and reference tumor mutation profiles for which subtypes have been predefined, NBS2 is trained by adjusting the weights on interaction features such that network propagation best recovers the provided subtypes. After training, weights are fixed such that mutation profiles of new tumors can be accurately classified. We evaluate NBS2 on breast and glioblastoma tumors, demonstrating that it outperforms the best network-based approaches in classifying tumors to known subtypes for these diseases. By interpreting the interaction weights, we highlight characteristic molecular pathways driving selected subtypes.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>The NBS2 package is freely available at: https://github.com/wzhang1984/NBSS.</jats:p> </jats:sec> <jats:sec> <jats:title>Supplementary information</jats:title> <jats:p>Supplementary data are available at Bioinformatics online.</jats:p> </jats:sec> Classifying tumors by supervised network propagation Bioinformatics |
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Bioinformatics |
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| title |
Classifying tumors by supervised network propagation |
| title_unstemmed |
Classifying tumors by supervised network propagation |
| title_full |
Classifying tumors by supervised network propagation |
| title_fullStr |
Classifying tumors by supervised network propagation |
| title_full_unstemmed |
Classifying tumors by supervised network propagation |
| title_short |
Classifying tumors by supervised network propagation |
| title_sort |
classifying tumors by supervised network propagation |
| topic |
Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| url |
http://dx.doi.org/10.1093/bioinformatics/bty247 |
| publishDate |
2018 |
| physical |
i484-i493 |
| description |
<jats:title>Abstract</jats:title>
<jats:sec>
<jats:title>Motivation</jats:title>
<jats:p>Network propagation has been widely used to aggregate and amplify the effects of tumor mutations using knowledge of molecular interaction networks. However, propagating mutations through interactions irrelevant to cancer leads to erosion of pathway signals and complicates the identification of cancer subtypes.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Results</jats:title>
<jats:p>To address this problem we introduce a propagation algorithm, Network-Based Supervised Stratification (NBS2), which learns the mutated subnetworks underlying tumor subtypes using a supervised approach. Given an annotated molecular network and reference tumor mutation profiles for which subtypes have been predefined, NBS2 is trained by adjusting the weights on interaction features such that network propagation best recovers the provided subtypes. After training, weights are fixed such that mutation profiles of new tumors can be accurately classified. We evaluate NBS2 on breast and glioblastoma tumors, demonstrating that it outperforms the best network-based approaches in classifying tumors to known subtypes for these diseases. By interpreting the interaction weights, we highlight characteristic molecular pathways driving selected subtypes.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Availability and implementation</jats:title>
<jats:p>The NBS2 package is freely available at: https://github.com/wzhang1984/NBSS.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Supplementary information</jats:title>
<jats:p>Supplementary data are available at Bioinformatics online.</jats:p>
</jats:sec> |
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| author | Zhang, Wei, Ma, Jianzhu, Ideker, Trey |
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| description | <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Motivation</jats:title> <jats:p>Network propagation has been widely used to aggregate and amplify the effects of tumor mutations using knowledge of molecular interaction networks. However, propagating mutations through interactions irrelevant to cancer leads to erosion of pathway signals and complicates the identification of cancer subtypes.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>To address this problem we introduce a propagation algorithm, Network-Based Supervised Stratification (NBS2), which learns the mutated subnetworks underlying tumor subtypes using a supervised approach. Given an annotated molecular network and reference tumor mutation profiles for which subtypes have been predefined, NBS2 is trained by adjusting the weights on interaction features such that network propagation best recovers the provided subtypes. After training, weights are fixed such that mutation profiles of new tumors can be accurately classified. We evaluate NBS2 on breast and glioblastoma tumors, demonstrating that it outperforms the best network-based approaches in classifying tumors to known subtypes for these diseases. By interpreting the interaction weights, we highlight characteristic molecular pathways driving selected subtypes.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>The NBS2 package is freely available at: https://github.com/wzhang1984/NBSS.</jats:p> </jats:sec> <jats:sec> <jats:title>Supplementary information</jats:title> <jats:p>Supplementary data are available at Bioinformatics online.</jats:p> </jats:sec> |
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| spelling | Zhang, Wei Ma, Jianzhu Ideker, Trey 1367-4803 1367-4811 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/bty247 <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Motivation</jats:title> <jats:p>Network propagation has been widely used to aggregate and amplify the effects of tumor mutations using knowledge of molecular interaction networks. However, propagating mutations through interactions irrelevant to cancer leads to erosion of pathway signals and complicates the identification of cancer subtypes.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>To address this problem we introduce a propagation algorithm, Network-Based Supervised Stratification (NBS2), which learns the mutated subnetworks underlying tumor subtypes using a supervised approach. Given an annotated molecular network and reference tumor mutation profiles for which subtypes have been predefined, NBS2 is trained by adjusting the weights on interaction features such that network propagation best recovers the provided subtypes. After training, weights are fixed such that mutation profiles of new tumors can be accurately classified. We evaluate NBS2 on breast and glioblastoma tumors, demonstrating that it outperforms the best network-based approaches in classifying tumors to known subtypes for these diseases. By interpreting the interaction weights, we highlight characteristic molecular pathways driving selected subtypes.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>The NBS2 package is freely available at: https://github.com/wzhang1984/NBSS.</jats:p> </jats:sec> <jats:sec> <jats:title>Supplementary information</jats:title> <jats:p>Supplementary data are available at Bioinformatics online.</jats:p> </jats:sec> Classifying tumors by supervised network propagation Bioinformatics |
| spellingShingle | Zhang, Wei, Ma, Jianzhu, Ideker, Trey, Bioinformatics, Classifying tumors by supervised network propagation, Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| title | Classifying tumors by supervised network propagation |
| title_full | Classifying tumors by supervised network propagation |
| title_fullStr | Classifying tumors by supervised network propagation |
| title_full_unstemmed | Classifying tumors by supervised network propagation |
| title_short | Classifying tumors by supervised network propagation |
| title_sort | classifying tumors by supervised network propagation |
| title_unstemmed | Classifying tumors by supervised network propagation |
| topic | Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| url | http://dx.doi.org/10.1093/bioinformatics/bty247 |