Dopcc: Detecting overlapping protein complexes via multi-metrics and co-core attachment method.

Identification of protein complex is an important issue in the field of system biology, which is crucial to understanding the cellular organization and inferring protein functions. Recently, many computational methods have been proposed to detect protein complexes from protein-protein interaction (PPI) networks. However, most of these methods only focus on local information of proteins in the PPI network, which are easily affected by the noise in the PPI network. Meanwhile, it's still challenging to detect protein complexes, especially for overlapping cases. To address these issues, we propose a new method, named Dopcc, to detect overlapping protein complexes by constructing a multi-metrics network according to different strategies. First, we adopt the Jaccard coefficient to measure the neighbor similarity between proteins and denoise the PPI network. Then, we propose a new strategy, integrating hierarchical compressing with network embedding, to capture the high-order structural similarity between proteins. Further, a new co-core attachment strategy is proposed to detect overlapping protein complexes from multi-metrics. The experimental results show that our proposed method, Dopcc, outperforms the other eight state-of-the-art methods in terms of F-measure, MMR, and Composite Score on two yeast datasets. The source code and datasets can be downloaded from https://github.com/CSUBioGroup/Dopcc.

CACO: A Core-Attachment Method With Cross-Species Functional Ortholog Information to Detect Human Protein Complexes.

Protein complexes play an essential role in living cells. Detecting protein complexes is crucial to understand protein functions and treat complex diseases. Due to high time and resource consumption of experiment approaches, many computational approaches have been proposed to detect protein complexes. However, most of them are only based on protein-protein interaction (PPI) networks, which heavily suffer from the noise in PPI networks. Therefore, we propose a novel core-attachment method, named CACO, to detect human protein complexes, by integrating the functional information from other species via protein ortholog relations. First, CACO constructs a cross-species ortholog relation matrix and transfers GO terms from other species as a reference to evaluate the confidence of PPIs. Then, a PPI filter strategy is adopted to clean the PPI network and thus a weighted clean PPI network is constructed. Finally, a new effective core-attachment algorithm is proposed to detect protein complexes from the weighted PPI network. Compared to other thirteen state-of-the-art methods, CACO outperforms all of them in terms of F-measure and Composite Score, showing that integrating ortholog information and the proposed core-attachment algorithm are effective in detecting protein complexes.

HyMM: hybrid method for disease-gene prediction by integrating multiscale module structure.

MOTIVATION: Identifying disease-related genes is an important issue in computational biology. Module structure widely exists in biomolecule networks, and complex diseases are usually thought to be caused by perturbations of local neighborhoods in the networks, which can provide useful insights for the study of disease-related genes. However, the mining and effective utilization of the module structure is still challenging in such issues as a disease gene prediction. RESULTS: We propose a hybrid disease-gene prediction method integrating multiscale module structure (HyMM), which can utilize multiscale information from local to global structure to more effectively predict disease-related genes. HyMM extracts module partitions from local to global scales by multiscale modularity optimization with exponential sampling, and estimates the disease relatedness of genes in partitions by the abundance of disease-related genes within modules. Then, a probabilistic model for integration of gene rankings is designed in order to integrate multiple predictions derived from multiscale module partitions and network propagation, and a parameter estimation strategy based on functional information is proposed to further enhance HyMM's predictive power. By a series of experiments, we reveal the importance of module partitions at different scales, and verify the stable and good performance of HyMM compared with eight other state-of-the-arts and its further performance improvement derived from the parameter estimation. CONCLUSIONS: The results confirm that HyMM is an effective framework for integrating multiscale module structure to enhance the ability to predict disease-related genes, which may provide useful insights for the study of the multiscale module structure and its application in such issues as a disease-gene prediction.

DPCMNE: Detecting Protein Complexes From Protein-Protein Interaction Networks Via Multi-Level Network Embedding.

Biological functions of a cell are typically carried out through protein complexes. The detection of protein complexes is therefore of great significance for understanding the cellular organizations and protein functions. In the past decades, many computational methods have been proposed to detect protein complexes. However, most of the existing methods just search the local topological information to mine dense subgraphs as protein complexes, ignoring the global topological information. To tackle this issue, we propose the DPCMNE method to detect protein complexes via multi-level network embedding. It can preserve both the local and global topological information of biological networks. First, DPCMNE employs a hierarchical compressing strategy to recursively compress the input protein-protein interaction (PPI) network into multi-level smaller PPI networks. Then, a network embedding method is applied on these smaller PPI networks to learn protein embeddings of different levels of granularity. The embeddings learned from all the compressed PPI networks are concatenated to represent the final protein embeddings of the original input PPI network. Finally, a core-attachment based strategy is adopted to detect protein complexes in the weighted PPI network constructed by the pairwise similarity of protein embeddings. To assess the efficiency of our proposed method, DPCMNE is compared with other eight clustering algorithms on two yeast datasets. The experimental results show that the performance of DPCMNE outperforms those state-of-the-art complex detection methods in terms of F1 and F1+Acc. Furthermore, the results of functional enrichment analysis indicate that protein complexes detected by DPCMNE are more biologically significant in terms of P-score.

Identification of Protein Complexes by Using a Spatial and Temporal Active Protein Interaction Network.

The rapid development of proteomics and high-throughput technologies has produced a large amount of Protein-Protein Interaction (PPI) data, which makes it possible for considering dynamic properties of protein interaction networks (PINs) instead of static properties. Identification of protein complexes from dynamic PINs becomes a vital scientific problem for understanding cellular life in the post genome era. Up to now, plenty of models or methods have been proposed for the construction of dynamic PINs to identify protein complexes. However, most of the constructed dynamic PINs just focus on the temporal dynamic information and thus overlook the spatial dynamic information of the complex biological systems. To address the limitation of the existing dynamic PIN analysis approaches, in this paper, we propose a new model-based scheme for the construction of the Spatial and Temporal Active Protein Interaction Network (ST-APIN) by integrating time-course gene expression data and subcellular location information. To evaluate the efficiency of ST-APIN, the commonly used classical clustering algorithm MCL is adopted to identify protein complexes from ST-APIN and the other three dynamic PINs, NF-APIN, DPIN, and TC-PIN. The experimental results show that, the performance of MCL on ST-APIN outperforms those on the other three dynamic PINs in terms of matching with known complexes, sensitivity, specificity, and f-measure. Furthermore, we evaluate the identified protein complexes by Gene Ontology (GO) function enrichment analysis. The validation shows that the identified protein complexes from ST-APIN are more biologically significant. This study provides a general paradigm for constructing the ST-APINs, which is essential for further understanding of molecular systems and the biomedical mechanism of complex diseases.