Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles

Yingtao Bi; Hyunsoo Kim; Ravi Gupta; Ramana V. Davuluri

doi:10.1371/journal.pone.0024210

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Open Access

Peer-reviewed

Research Article

Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles

Yingtao Bi,

Affiliation Molecular and Cellular Oncogenesis Program, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
⨯
Hyunsoo Kim,

Affiliation Molecular and Cellular Oncogenesis Program, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
⨯
Ravi Gupta,

Affiliation Molecular and Cellular Oncogenesis Program, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
⨯
Ramana V. Davuluri

* E-mail: rdavuluri@wistar.org

Affiliation Molecular and Cellular Oncogenesis Program, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
⨯

Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles

Yingtao Bi,
Hyunsoo Kim,
Ravi Gupta,
Ramana V. Davuluri

Published: September 2, 2011
https://doi.org/10.1371/journal.pone.0024210

About the Authors

Yingtao Bi

Affiliation Molecular and Cellular Oncogenesis Program, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania, United States of America

Hyunsoo Kim

Affiliation Molecular and Cellular Oncogenesis Program, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania, United States of America

Ravi Gupta

Affiliation Molecular and Cellular Oncogenesis Program, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania, United States of America

Ramana V. Davuluri

* E-mail: rdavuluri@wistar.org

Affiliation Molecular and Cellular Oncogenesis Program, Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, Pennsylvania, United States of America

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Wrote the paper: YB RVD. Conceived of the project: YB RVD. Implemented the algorithm: YB. Tested the algorithm: YB HK RG. Provided guidance for the project: RVD.

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Sequence motif analysis
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Chipmunks
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Transcription factors
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Simulation and modeling
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Nucleotide sequencing
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Nucleotides
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Markov models
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DNA transcription
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