title: Detection of overlapping protein complexes in gene expression, phenotype and pathways of Saccharomyces cerevisiae using Prorank based Fuzzy algorithm.
abstract: Proteins show their functional activity by interacting with other proteins and forms protein complexes since it is playing an important role in cellular organization and function. To understand the higher order protein organization, overlapping is an important step towards unveiling functional and evolutionary mechanisms behind biological networks. Most of the clustering algorithms do not consider the weighted as well as overlapping complexes. In this research, Prorank based Fuzzy algorithm has been proposed to find the overlapping protein complexes. The Fuzzy detection algorithm is incorporated in the Prorank algorithm after ranking step to find the overlapping community. The proposed algorithm executes in an iterative manner to compute the probability of robust clusters. The proposed and the existing algorithms were tested on different datasets such as PPI-D1, PPI-D2, Collins, DIP, Krogan Core and Krogan-Extended, gene expression such as GSE7645, GSE22269, GSE26923, pathways such as Meiosis, MAPK, Cell Cycle, phenotypes such as Yeast Heterogeneous and Yeast Homogeneous datasets. The experimental results show that the proposed algorithm predicts protein complexes with better accuracy compared to other state of art algorithms.
authors.affiliation: Department of Computer Science, Bharathiar University, Coimbatore 641 046, India. Electronic address: manimkn89@gmail.com.
authors.forename: P
authors.initials: P
authors.lastname: Manikandan
authors.affiliation: Department of Computer Science, Bharathiar University, Coimbatore 641 046, India.
authors.forename: D
authors.initials: D
authors.lastname: Ramyachitra
authors.affiliation: Department of Computer Science, Bharathiar University, Coimbatore 641 046, India.
authors.forename: D
authors.initials: D
authors.lastname: Banupriya
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D017143:Fuzzy Logic; D015966:Gene Expression Regulation, Fungal; D046912:Multiprotein Complexes / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D010641:Phenotype; D025941:Protein Interaction Mapping / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D015398:Signal Transduction / Q000235:genetics
chemical_list: D005656:Fungal Proteins; D046912:Multiprotein Complexes
keywords: Overlapping; Protein complex detection; Proteins; Protein–protein interaction