Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors

Daifeng Wang; Koon-Kiu Yan; Cristina Sisu; Chao Cheng; Joel Rozowsky; William Meyerson; Mark B. Gerstein

doi:10.1371/journal.pcbi.1004132

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Peer-reviewed

Research Article

Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors

Daifeng Wang,

Affiliations Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
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Koon-Kiu Yan,

Affiliations Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
⨯
Cristina Sisu,

Affiliations Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
⨯
Chao Cheng,

Affiliation Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
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Joel Rozowsky,

Affiliations Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
⨯
William Meyerson,

Affiliation School of Medicine, Yale University, New Haven, Connecticut, United States of America
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Mark B. Gerstein

* E-mail: mark@gersteinlab.org

Affiliations Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America, Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
⨯

Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors

Daifeng Wang,
Koon-Kiu Yan,
Cristina Sisu,
Chao Cheng,
Joel Rozowsky,
William Meyerson,
Mark B. Gerstein

Published: April 17, 2015
https://doi.org/10.1371/journal.pcbi.1004132

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A comment about the Yeast application

Posted by Alizad-Rahvar on 18 Nov 2018 at 08:05 GMT

In the case of your application for Yeast, my understanding is that you have considered all available TF-TF-tar-
get triplets and investigated if it is consistent with a gate or not. My question is that, if 3 TFs are regulating a target gene cooperatively and simultaneously, you should probably have 3 different TF-TF-tar-
get triplets for them (TF1-TF2-target, TF1-TF3-target, and TF2-TF3-target). In this case, since you have not considered one of the TFs in each triplet, your detected gate cannot be correct (it can easily happen for the target genes that you have found more than one triplet for them).
Any comment?!

No competing interests declared.

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Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors

Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors

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A comment about the Yeast application

Posted by Alizad-Rahvar on 18 Nov 2018 at 08:05 GMT