Dataset Information

Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins.

ABSTRACT:

Unlabelled

: We introduce Path2PPI, a new R package to identify protein-protein interaction (PPI) networks for fully sequenced organisms for which nearly none PPI are known. Path2PPI predicts PPI networks based on sets of proteins from well-established model organisms, providing an intuitive visualization and usability. It can be used to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism.

Availability and implementation

Path2PPI is an open-source tool implemented in R. It can be obtained from the Bioconductor project: http://bioconductor.org/packages/Path2PPI/ CONTACT: : ina.koch@bioinformatik.uni-frankfurt.de

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Philipp O

PROVIDER: S-EPMC4848400 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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Publications

Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins.

Philipp Oliver O Osiewacz Heinz D HD Koch Ina I

Bioinformatics (Oxford, England) 20160105 9

<h4>Unlabelled</h4>: We introduce Path2PPI, a new R package to identify protein-protein interaction (PPI) networks for fully sequenced organisms for which nearly none PPI are known. Path2PPI predicts PPI networks based on sets of proteins from well-established model organisms, providing an intuitive visualization and usability. It can be used to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism.<h4>Availability and ...[more]

PMID: 26733452

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Project description:BackgroundIdentification of essential proteins plays a significant role in understanding minimal requirements for the cellular survival and development. Many computational methods have been proposed for predicting essential proteins by using the topological features of protein-protein interaction (PPI) networks. However, most of these methods ignored intrinsic biological meaning of proteins. Moreover, PPI data contains many false positives and false negatives. To overcome these limitations, recently many research groups have started to focus on identification of essential proteins by integrating PPI networks with other biological information. However, none of their methods has widely been acknowledged.ResultsBy considering the facts that essential proteins are more evolutionarily conserved than nonessential proteins and essential proteins frequently bind each other, we propose an iteration method for predicting essential proteins by integrating the orthology with PPI networks, named by ION. Differently from other methods, ION identifies essential proteins depending on not only the connections between proteins but also their orthologous properties and features of their neighbors. ION is implemented to predict essential proteins in S. cerevisiae. Experimental results show that ION can achieve higher identification accuracy than eight other existing centrality methods in terms of area under the curve (AUC). Moreover, ION identifies a large amount of essential proteins which have been ignored by eight other existing centrality methods because of their low-connectivity. Many proteins ranked in top 100 by ION are both essential and belong to the complexes with certain biological functions. Furthermore, no matter how many reference organisms were selected, ION outperforms all eight other existing centrality methods. While using as many as possible reference organisms can improve the performance of ION. Additionally, ION also shows good prediction performance in E. coli K-12.ConclusionsThe accuracy of predicting essential proteins can be improved by integrating the orthology with PPI networks.

Project description:BackgroundIdentifying similarities and differences in the molecular constitutions of various types of cancer is one of the key challenges in cancer research. The appearances of a cancer depend on complex molecular interactions, including gene regulatory networks and gene-environment interactions. This complexity makes it challenging to decipher the molecular origin of the cancer. In recent years, many studies reported methods to uncover heterogeneous depictions of complex cancers, which are often categorized into different subtypes. The challenge is to identify diverse molecular contexts within a cancer, to relate them to different subtypes, and to learn underlying molecular interactions specific to molecular contexts so that we can recommend context-specific treatment to patients.ResultsIn this study, we describe a novel method to discern molecular interactions specific to certain molecular contexts. Unlike conventional approaches to build modular networks of individual genes, our focus is to identify cancer-generic and subtype-specific interactions between contextual gene sets, of which each gene set share coherent transcriptional patterns across a subset of samples, termed contextual gene set. We then apply a novel formulation for quantitating the effect of the samples from each subtype on the calculated strength of interactions observed. Two cancer data sets were analyzed to support the validity of condition-specificity of identified interactions. When compared to an existing approach, the proposed method was much more sensitive in identifying condition-specific interactions even in heterogeneous data set. The results also revealed that network components specific to different types of cancer are related to different biological functions than cancer-generic network components. We found not only the results that are consistent with previous studies, but also new hypotheses on the biological mechanisms specific to certain cancer types that warrant further investigations.ConclusionsThe analysis on the contextual gene sets and characterization of networks of interaction composed of these sets discovered distinct functional differences underlying various types of cancer. The results show that our method successfully reveals many subtype-specific regions in the identified maps of biological contexts, which well represent biological functions that can be connected to specific subtypes.

Dataset Information

Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins.

Unlabelled

Availability and implementation

Supplementary information

Publications

Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins.

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