PCD-GED: Protein complex detection considering PPI dynamics based on time series gene expression data

Protein complex identification based on weighted PPI network with multi-source information

“…So far, density-based clustering ( Adamcsek et al, 2006 ;Altaf-Ul-Amin et al, 2006 ;Bader and Hogue, 2003 ), hierarchical clustering ( Ahn et al, 2010 ;Arnau et al, 2005 ), partition-based clustering ( BJ and D., 2007 ;King et al, 2004 ), flow simulation-based clustering ( Enright et al, 2002 ;Pereira-Leal et al, 2004 ;Cho et al, 2007 ) and other methods ( Hwang et al, 2008 ;Inoue et al, 2010 ;Lecca and Re , 2015 ;Nepusz et al, 2012 ;Wu et al, 2009 ;Yu et al, 2015a ;Liu et al, 2017 ;Maddi and Eslahchi, 2017 ) have been proposed to detect protein clusters based on the PPI data. In addition, the source of necessary biological information has been used to locate protein complexes in PPI networks ( Andreopoulos et al, 2009 ;Lakizadeh et al, 2015 ) effectively. There is a common problem among these methods, in that way the node is just one dimensional vertex in the network without considering other biological information hidden in the node (protein).…”

Predicting Protein Complexes in Weighted Dynamic PPI Networks Based on ICSC

“…Biological functions of cells are carried out by protein complexes rather than single proteins [1]. Detecting these protein complexes can help to predict protein functions and explain biological processes, which has great significance in biology, pathology, and proteomics [2]. Therefore, the study of protein complexes has become one of most important subjects.…”

Combining sequence and Gene Ontology for protein module detection in the Weighted Network

“…In recent years, a number of new approaches (Hwang et al, 2008;Inoue et al, 2010;Lecca and Re, 2015;Nepusz et al, 2012;Wu et al, 2009;Yu et al, 2015), utilizing some novel computational models to identify protein modules in a PPI network, has been emerging. Especially, the sources of other biological information have been recently employed to the detection of protein modules in PPI networks (Andreopoulos et al, 2009;Feng et al, 2010;Kouhsar et al, 2016;Lakizadeh et al, 2015;Li et al, 2015;Maraziotis et al, 2007). Though using computational approaches to detect protein functional modules in PPI networks has received considerable attention and researchers have proposed many detection ideas and schemes over the past few years, how to efficiently identify protein modules by means of multiple sources of biological information is still a vital and challenging scientific problem in computational biology.…”