In silico determination of protein complexes in yeast

Abstract

In this thesis, the protein complexes in an interaction network of 20,487 interactions between 4,944 proteins were determined by the integration of different biological datasets. We recruit different data sources that include co-expression measures (PCCA), interaction data (TI), and GO process (PSA), function (FSA) and localization similarity (LSA) information and CFinder algorithm to identify highly interactive modules in the interaction network. Due to the dense interactions inside a community, among 4944 proteins, CFinder could only clustered 1822 proteins inside one or more community. Among the 55 communities investigated, according to the cut-off value that was selected (0.64), 20 communities had FF value greater than 0.64 and all of the 20 communities were protein complexes or part of the complexes. 11 different complexes were found, 9 of them; nuclear exosome (NE), anaphase promoting complex (APC), transport protein particle (TRAPP), mRNA cleavage factor (mRNACF), RSC, spliceosomal uridine-rich small nuclear ribonucleoprotein (snRNP U1), mediator (M), ARP2/3, Transcriptional elongation factor (TEF) are transient complexes. Two of them, proteasome regulatory particle (PRP) and DNA directed RNA polymerase II complex (RNA 2) are permanent complexes. These 11 complexes contain overall 295 proteins. The total community frequency is 94.8%; 128 out of 135 proteins of k-clique communities are members of the complexes. % 100 of the proteins of the TRAPP complex is identified with a community frequency of 100 %.11 proteins of the APC complex was identified. 13 proteins of mRNACF were detected by the community k9.4 with a community frequency of %100. Transcriptional elongation factor consists in total of 19 proteins (SGD). We identified 7 proteins of transcriptional elongation factor in the community k7.1. Mediator complex consists of 20 proteins (SGD), and we identified 7 proteins of M with a community frequency of 100% in the community k7.6 PRP consist of 22 proteins (SGD).We identified 11 members of the PRP complex out of 12 proteins in community k10.4 and 14 members of PRP complex out of 16 proteins in column k9.6. Six components out of 8 proteins of k8.8 are the members of the RNA 2 complex.