کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
6368807 1623798 2017 6 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Combining sequence and Gene Ontology for protein module detection in the Weighted Network
ترجمه فارسی عنوان
ترکیبی از توالی و هسته شناسی ژنتیک برای تشخیص ماژول پروتئین در شبکه وزن
کلمات کلیدی
پروتئین پیچیده، تعامل پروتئین، آنتولوژی ژنی، شبکه توزیع،
موضوعات مرتبط
علوم زیستی و بیوفناوری علوم کشاورزی و بیولوژیک علوم کشاورزی و بیولوژیک (عمومی)
چکیده انگلیسی


- Sequence and gene ontology are combined for protein complex detection.
- The weighted graphs based on gene ontology and PPI network are constructed.
- In the clustering part, density, diameter and the included angle cosine are employed for locating candidate complexes.
- The experimental results show that the proposed method can generally perform better than five useful methods in forms of recall and f-measure.

Studies of protein modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in locating protein modules. In this paper, a new approach combining Gene Ontology and amino acid background frequency is introduced to detect the protein modules in the weighted PPI networks. The proposed approach mainly consists of three parts: the feature extraction, the weighted graph construction and the protein complex detection. Firstly, the topology-sequence information is utilized to present the feature of protein complex. Secondly, six types of the weighed graph are constructed by combining PPI network and Gene Ontology information. Lastly, protein complex algorithm is applied to the weighted graph, which locates the clusters based on three conditions, including density, network diameter and the included angle cosine. Experiments have been conducted on two protein complex benchmark sets for yeast and the results show that the approach is more effective compared to five typical algorithms with the performance of f-measure and precision. The combination of protein interaction network with sequence and gene ontology data is helpful to improve the performance and provide a optional method for protein module detection.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Theoretical Biology - Volume 412, 7 January 2017, Pages 107-112
نویسندگان
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