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Rechecking the Centrality-Lethality Rule in the Scope of Protein Subcellular Localization Interaction Networks.

Peng X, Wang J, Wang J, Wu FX, Pan Y - PLoS ONE (2015)

Bottom Line: However, neglecting the temporal and spatial features of protein-protein interactions, the centrality scores calculated by centrality methods are not effective enough for measuring the essentiality of proteins in a PIN.It indicates that proteins with high LCSs measured from PSLINs are more likely to be essential and the performance of centrality methods can be improved by LSED.Furthermore, LSED provides a wide applicable prediction model to identify essential proteins for different species.

View Article: PubMed Central - PubMed

Affiliation: School of Information Science and Engineering, Central South University, Changsha, Hunan, 410083, China.

ABSTRACT
Essential proteins are indispensable for living organisms to maintain life activities and play important roles in the studies of pathology, synthetic biology, and drug design. Therefore, besides experiment methods, many computational methods are proposed to identify essential proteins. Based on the centrality-lethality rule, various centrality methods are employed to predict essential proteins in a Protein-protein Interaction Network (PIN). However, neglecting the temporal and spatial features of protein-protein interactions, the centrality scores calculated by centrality methods are not effective enough for measuring the essentiality of proteins in a PIN. Moreover, many methods, which overfit with the features of essential proteins for one species, may perform poor for other species. In this paper, we demonstrate that the centrality-lethality rule also exists in Protein Subcellular Localization Interaction Networks (PSLINs). To do this, a method based on Localization Specificity for Essential protein Detection (LSED), was proposed, which can be combined with any centrality method for calculating the improved centrality scores by taking into consideration PSLINs in which proteins play their roles. In this study, LSED was combined with eight centrality methods separately to calculate Localization-specific Centrality Scores (LCSs) for proteins based on the PSLINs of four species (Saccharomyces cerevisiae, Homo sapiens, Mus musculus and Drosophila melanogaster). Compared to the proteins with high centrality scores measured from the global PINs, more proteins with high LCSs measured from PSLINs are essential. It indicates that proteins with high LCSs measured from PSLINs are more likely to be essential and the performance of centrality methods can be improved by LSED. Furthermore, LSED provides a wide applicable prediction model to identify essential proteins for different species.

No MeSH data available.


Related in: MedlinePlus

The schematic of LSED method.
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pone.0130743.g001: The schematic of LSED method.

Mentions: The LSED method mainly contains four steps, as shown in Fig 1. Given a global PIN and subcellular localization information of proteins, firstly, a PSLIN was constructed for each subcellular localization. Secondly, the confidence level of each PSLIN is calculated according to the size of the PSLIN. In the third step, a centrality method is applied to each PSLIN for calculating the centrality scores of proteins in the PSLIN. Then the LCS of each protein is calculated based on its centrality scores in different PSLINs and the confidence levels of these PSLINs. Finally, the proteins are sorted by their LCSs in descending order. The details of each step will be discussed in the following subsections.


Rechecking the Centrality-Lethality Rule in the Scope of Protein Subcellular Localization Interaction Networks.

Peng X, Wang J, Wang J, Wu FX, Pan Y - PLoS ONE (2015)

The schematic of LSED method.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482623&req=5

pone.0130743.g001: The schematic of LSED method.
Mentions: The LSED method mainly contains four steps, as shown in Fig 1. Given a global PIN and subcellular localization information of proteins, firstly, a PSLIN was constructed for each subcellular localization. Secondly, the confidence level of each PSLIN is calculated according to the size of the PSLIN. In the third step, a centrality method is applied to each PSLIN for calculating the centrality scores of proteins in the PSLIN. Then the LCS of each protein is calculated based on its centrality scores in different PSLINs and the confidence levels of these PSLINs. Finally, the proteins are sorted by their LCSs in descending order. The details of each step will be discussed in the following subsections.

Bottom Line: However, neglecting the temporal and spatial features of protein-protein interactions, the centrality scores calculated by centrality methods are not effective enough for measuring the essentiality of proteins in a PIN.It indicates that proteins with high LCSs measured from PSLINs are more likely to be essential and the performance of centrality methods can be improved by LSED.Furthermore, LSED provides a wide applicable prediction model to identify essential proteins for different species.

View Article: PubMed Central - PubMed

Affiliation: School of Information Science and Engineering, Central South University, Changsha, Hunan, 410083, China.

ABSTRACT
Essential proteins are indispensable for living organisms to maintain life activities and play important roles in the studies of pathology, synthetic biology, and drug design. Therefore, besides experiment methods, many computational methods are proposed to identify essential proteins. Based on the centrality-lethality rule, various centrality methods are employed to predict essential proteins in a Protein-protein Interaction Network (PIN). However, neglecting the temporal and spatial features of protein-protein interactions, the centrality scores calculated by centrality methods are not effective enough for measuring the essentiality of proteins in a PIN. Moreover, many methods, which overfit with the features of essential proteins for one species, may perform poor for other species. In this paper, we demonstrate that the centrality-lethality rule also exists in Protein Subcellular Localization Interaction Networks (PSLINs). To do this, a method based on Localization Specificity for Essential protein Detection (LSED), was proposed, which can be combined with any centrality method for calculating the improved centrality scores by taking into consideration PSLINs in which proteins play their roles. In this study, LSED was combined with eight centrality methods separately to calculate Localization-specific Centrality Scores (LCSs) for proteins based on the PSLINs of four species (Saccharomyces cerevisiae, Homo sapiens, Mus musculus and Drosophila melanogaster). Compared to the proteins with high centrality scores measured from the global PINs, more proteins with high LCSs measured from PSLINs are essential. It indicates that proteins with high LCSs measured from PSLINs are more likely to be essential and the performance of centrality methods can be improved by LSED. Furthermore, LSED provides a wide applicable prediction model to identify essential proteins for different species.

No MeSH data available.


Related in: MedlinePlus