NIBNA: a network-based node importance approach for identifying breast cancer drivers.

Complex networks have in generally communities. These communities are very important. Network’s communities represent sets of nodes, which are very connected. In this research, we developed a new method to find the community structure in networks. Our method is based on flower pollination algorithm (FPA) witch is used in the splitting process. The splitting of networks in our method maximizes a function of quality called modularity. We provide a general framework for implementing our new method to find community structure in networks. We present the effectiveness of our method by comparison with some known methods on computer-generated and real-world networks.

When studying dynamic networks, it is often of interest to understand how the community structure of the network changes. However, before studying the community structure of dynamic social networks, one must first collect appropriate network data. In this paper we present a network sampling technique to crawl the community structure of dynamic networks when there is a limitation on the number of nodes that can be queried. The process begins by obtaining a sample for the first time step. In subsequent time steps, the crawling process is guided by community structure discoveries made in the past. Experiments conducted on the proposed approach and certain baseline techniques reveal the proposed approach has at least 35% performance increase in cases when the total query budget is fixed over the entire period and at least 8% increase in cases when the query budget is fixed per time step.

Identifying cancer driver genes is an important task in cancer research. Numerous methods that identify these driver genes have been proposed, most of which identify driver genes in entire patient cohorts. However, research has shown that cancers in different patients may be caused by different driver genes. Therefore, if we pay more attention to the individual level to identify personalized driver genes, patients can receive precise treatment and achieve better treatment results. Among the methods for identifying personalized cancer drivers, most of these methods only identify the coding driver genes, however, non-coding cancer drivers are also crucial for the initialization and development of cancer. Therefore, we develop an approach to identify coding drivers and non-coding drivers for individual patients named PerVote. In PerVote, the personalized network is firstly constructed based on expression data of mRNAs and miRNAs, then identifies cancer drivers by a voting approach in the network. To verify the performance of our method, we use five cancer datasets of TCGA and compare it with the state-of-the-art methods. The results show that PerVote outperforms other methods. Our method also predicts and prioritizes miRNA drivers, most of which are confirmed by OncomiR to be related to tumorigenesis. Therefore, PerVote can bring further help to the personalized treatment of cancer patients and is an effective method for the identification of cancer drivers.KeywordCancerPersonalized driver genesInteraction networkVoting mechanism

Identifying and evaluating community structure in complex networks

In reality many complex networks present modules or community structures obviously. Modularity is a benefit function used in quantifying the quality of a division of a network into communities. And it usually can be used as a basis for optimization methods of detecting community structure in networks. But the most popular modularity which is proposed by M. E. J. Newman and M. Girvan has the resolution limit in community detection. Multi-resolution modularity cannot overcome the misclassifications caused by merging and splitting the communities either. In this paper, we propose a multi-resolution density modularity based on the network density. The proposed function is tested on the artificial networks. Computational results show that it can reduce the rate of misclassification considerably. And the systematicness of the community structures can be demonstrated by the multi-resolution density modularity.

Networks have become a widely used tool for modeling complex systems in many different fields. This approach is extremely useful for representing interactions among genes, social relationships, Internet communications or correlations of prices within a stock market, to name just a few examples. By analyzing the structure of these networks and understanding how their different elements interact, we could improve our knowledge of the whole system. Usually, nodes that compose these networks tend to create tightly knit groups. This property, of high interest in many scientific fields, is called community structure and improving its detection and characterization is what this thesis is all about. The first objective of this work is the generation of efficient methods able to characterize the communities of a network and to understand its structure. Second, we will try to create a set of tests where such methods can be studied. Finally, we will suggest a statistical measure in order to be able to properly assess the quality of the community structure of a network. To accomplish these objectives, first, we generate a set of algorithms that can transform a network into a hierarchical tree and, from there, to determine their most relevant communities. Furthermore, we have developed a new type of benchmarks for effectively testing these and other community detection algorithms. Finally, and as the most important contribution of this work, it is shown that the community structure of a network can be accurately evaluated using a hypergeometric distribution-based index. Thus, the maximization of this measure, called Surprise, appears as the best proposed strategy for detecting the optimal partition into communities of a network. Surprise exhibits an excellent behavior in all networks analyzed, qualitatively outperforming any previous method. Thus, it appears as the best measure proposed to this end and the data suggests that it could be an optimal strategy to determine the quality of the community structure of complex networks.

Alterations in transcriptional networks in cancer: the role of noncoding somatic driver mutations

As an open issue, the measure of community influential is no uniform standard, how to measure the influence of community has attracted extensive attention. This paper proposed a quantitative measure to identify the influence of community. Based on the state of critical functionality (SCF), a new function, which names as the weighted state of critical functionality (WSCF), is defined. For the WSCF, not only the connections among communities but also the topology within community is considered. When the community structure of the complex network is divided, each community is renormalized as a node by the renormalization method. Then, the influence of community is measured by the values of WSCF, the greater the value of WSCF, the less the influence of the corresponding community. The influence of community of three classic constructed networks (i.e., a Erodös-Rényi (ER) random network, a BA scale free network and a small-word (SW) network) is measured by the proposed method. To further verify the feasibility of the method, two community detection algorithms are used to divide community structure in the real networks. The influence of the community of the 9/11 terrorist network, a US Air network and a PolBooks network is measured by the proposed method. The influence of each community could be measured and the most influential community in each network is identified by the proposed method. The results reveal that the proposed method is a feasible measure to identify the influence of community, its recognition effect is better than SCF, and accuracy is higher. The SCF is a special case of WSCF, when the weights and cluster coefficients are equal to 1. For the proposed method, once the community structure of the network is divided, the corresponding community influence is identified by the proposed method, which is not affected by the community division algorithms.

We present a reformulation of modularity that allows the analysis of the community structure in networks of correlated data. The modularity preserves the probabilistic semantics of the original definition even when the network is directed, weighted, signed, and has self-loops. This is the most general condition one can find in the study of any network, in particular those defined from correlated data. We apply our results to a real network of correlated data between stores in the city of Lyon (France).

Community detection via closure extension

Several approaches have been proposed to solve the well-studied problem of detecting community structure in networks. However, many existing algorithms encounter difficulties when the proportion of inter-community links is higher than the proportion of intra-community links. To overcome this situation, we propose a novel algorithm which performs community detection in two phases. The first phase exploits the covariance of links between nodes and the interclass inertia in order to perform an initial partitioning of the network. The objective is to generate small disconnected groups of nodes mostly from the same community. Then, in the second phase, we propose an iterative process that repeatedly merges these initial groups to identify the final community structure that maximizes the modularity. We illustrate the suitability of our proposal through an empirical study that uses both generated and real-life networks.

Non-coding mutations may drive cancer development. Statistical detection of non-coding driver regions is challenged by a varying mutation rate and uncertainty of functional impact. Here, we develop a statistically founded non-coding driver-detection method, ncdDetect, which includes sample-specific mutational signatures, long-range mutation rate variation, and position-specific impact measures. Using ncdDetect, we screened non-coding regulatory regions of protein-coding genes across a pan-cancer set of whole-genomes (n = 505), which top-ranked known drivers and identified new candidates. For individual candidates, presence of non-coding mutations associates with altered expression or decreased patient survival across an independent pan-cancer sample set (n = 5454). This includes an antigen-presenting gene (CD1A), where 5’UTR mutations correlate significantly with decreased survival in melanoma. Additionally, mutations in a base-excision-repair gene (SMUG1) correlate with a C-to-T mutational-signature. Overall, we find that a rich model of mutational heterogeneity facilitates non-coding driver identification and integrative analysis points to candidates of potential clinical relevance.DOI:http://dx.doi.org/10.7554/eLife.21778.001

Non-coding mutations may drive cancer development. Statistical detection of non-coding driver regions is challenged by a varying mutation rate and uncertainty of functional impact. Here, we develop a statistically founded non-coding driver-detection method, ncdDetect, which includes sample-specific mutational signatures, long-range mutation rate variation, and position-specific impact measures. Using ncdDetect, we screened non-coding regulatory regions of protein-coding genes across a pan-cancer set of whole-genomes (n = 505), which top-ranked known drivers and identified new candidates. For individual candidates, presence of non-coding mutations associates with altered expression or decreased patient survival across an independent pan-cancer sample set (n = 5454). This includes an antigen-presenting gene (CD1A), where 5'UTR mutations correlate significantly with decreased survival in melanoma. Additionally, mutations in a base-excision-repair gene (SMUG1) correlate with a C-to-T mutational-signature. Overall, we find that a rich model of mutational heterogeneity facilitates non-coding driver identification and integrative analysis points to candidates of potential clinical relevance.

In this paper, three new algorithms, a greedy algorithm, a KL-like algorithm, and an add-all algorithm, are proposed to find local optimal community structures in large networks starting from a given source vertex. The time complexity for finding a local community of all these algorithms is O(K 2d), where K is the number of vertices to be explored in the sub-graph and d is the average degree of the vertices in the sub-graph. A JAVA tool is developed based on these algorithms to identify local community structures in large networks. The results of using this tool to analyze a co-purchase network from Amazon.com show that local community structures exist in this large-scale co-purchase network. Further analyses of the identified local communities show that purchases of media items form more compact local communities than purchases of book items do, indicating that recommending digital media items to customers based on co-purchasing information in the online store is more efficient than recommending books.

Finding different types of communities has become a research hot spot in network science. Plenty of the real-world systems containing different types of objects and relationships can be perfectly described as the heterogeneous networks. However, most of the current research on community detection is applied for the homogeneous networks, while there is no effective function to quantify the quality of the community structure in heterogeneous networks. In this paper, we first propose the null model with the same heterogeneous node degree distribution of the original heterogeneous networks. The probability of there being an edge between two nodes is given to build the modularity function of the heterogeneous networks. Based on our modularity function, a fast algorithm of community detection is proposed for the large scale heterogeneous networks. We use the algorithm to detect the communities in the real-world twitter event networks. The experimental results show that our method perform better than other exciting algorithms and demonstrate that the modularity function of the heterogeneous networks is an effective parameter that can be used to quantify the quality of the community structure in heterogeneous networks.