DegSampler: Collapsed Gibbs sampler for detecting E3 binding sites

Osamu Maruyama; Fumiko Matsuzaki

doi:10.1109/BIBE.2018.00009

DegSampler: Collapsed Gibbs sampler for detecting E3 binding sites

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

In this paper, we address the problem of finding sequence motifs in substrate proteins specific to E3 ubiquitin ligases (E3s). We formulated a posterior probability distribution of sites by designing a likelihood function based on amino acid indexing and a prior distribution based on the disorderness of protein sequences. These designs are derived from known characteristics of E3 binding sites in substrate proteins. Then, we devise a collapsed Gibbs sampling algorithm for the posterior probability distribution called DegSampler. We performed computational experiments using 36 sets of substrate proteins specific to E3s and compared the performance of DegSampler with those of popular motif finders, MEME and GLAM2. The results showed that DegSampler was superior to the others in finding E3 binding motifs. Thus, DegSampler is a promising tool for finding E3 motifs in substrate proteins.

Original language	English
Title of host publication	Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	1-9
Number of pages	9
ISBN (Electronic)	9781538662168
DOIs	https://doi.org/10.1109/BIBE.2018.00009
Publication status	Published - Dec 6 2018
Event	18th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2018 - Taichung, Taiwan, Province of China Duration: Oct 29 2018 → Oct 31 2018

Publication series

Name	Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018

Other

Other	18th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2018
Country/Territory	Taiwan, Province of China
City	Taichung
Period	10/29/18 → 10/31/18

All Science Journal Classification (ASJC) codes

Genetics(clinical)
Health Informatics
Oncology
Biomedical Engineering
Cardiology and Cardiovascular Medicine

Access to Document

10.1109/BIBE.2018.00009

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Maruyama, O., & Matsuzaki, F. (2018). DegSampler: Collapsed Gibbs sampler for detecting E3 binding sites. In Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018 (pp. 1-9). Article 8567448 (Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBE.2018.00009

DegSampler: Collapsed Gibbs sampler for detecting E3 binding sites. / Maruyama, Osamu ; Matsuzaki, Fumiko.
Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018. Institute of Electrical and Electronics Engineers Inc., 2018. p. 1-9 8567448 (Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Maruyama, O & Matsuzaki, F 2018, DegSampler: Collapsed Gibbs sampler for detecting E3 binding sites. in Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018., 8567448, Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018, Institute of Electrical and Electronics Engineers Inc., pp. 1-9, 18th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2018, Taichung, Taiwan, Province of China, 10/29/18. https://doi.org/10.1109/BIBE.2018.00009

Maruyama O , Matsuzaki F. DegSampler: Collapsed Gibbs sampler for detecting E3 binding sites. In Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018. Institute of Electrical and Electronics Engineers Inc. 2018. p. 1-9. 8567448. (Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018). doi: 10.1109/BIBE.2018.00009

Maruyama, Osamu ; Matsuzaki, Fumiko. / DegSampler : Collapsed Gibbs sampler for detecting E3 binding sites. Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018. Institute of Electrical and Electronics Engineers Inc., 2018. pp. 1-9 (Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018).

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abstract = "In this paper, we address the problem of finding sequence motifs in substrate proteins specific to E3 ubiquitin ligases (E3s). We formulated a posterior probability distribution of sites by designing a likelihood function based on amino acid indexing and a prior distribution based on the disorderness of protein sequences. These designs are derived from known characteristics of E3 binding sites in substrate proteins. Then, we devise a collapsed Gibbs sampling algorithm for the posterior probability distribution called DegSampler. We performed computational experiments using 36 sets of substrate proteins specific to E3s and compared the performance of DegSampler with those of popular motif finders, MEME and GLAM2. The results showed that DegSampler was superior to the others in finding E3 binding motifs. Thus, DegSampler is a promising tool for finding E3 motifs in substrate proteins.",

author = "Osamu Maruyama and Fumiko Matsuzaki",

note = "Funding Information: This work was supported by JSPS KAKENHI Grant Number JP17K00407. Publisher Copyright: {\textcopyright} 2018 IEEE.; 18th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2018 ; Conference date: 29-10-2018 Through 31-10-2018",

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DegSampler: Collapsed Gibbs sampler for detecting E3 binding sites

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