scholarly journals Application of dynamic expansion tree for finding large network motifs in biological networks

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6917 ◽  
Author(s):  
Sabyasachi Patra ◽  
Anjali Mohapatra
Keyword(s):  
Biological Networks ◽  
Protein Function ◽  
Large Scale ◽  
Network Motif ◽  
Graph Isomorphism ◽  
Interaction Network ◽  
Motif Finding ◽  
Network Motifs ◽  
Large Network ◽  
Scalable Network

Network motifs play an important role in the structural analysis of biological networks. Identification of such network motifs leads to many important applications such as understanding the modularity and the large-scale structure of biological networks, classification of networks into super-families, and protein function annotation. However, identification of large network motifs is a challenging task as it involves the graph isomorphism problem. Although this problem has been studied extensively in the literature using different computational approaches, still there is a lot of scope for improvement. Motivated by the challenges involved in this field, an efficient and scalable network motif finding algorithm using a dynamic expansion tree is proposed. The novelty of the proposed algorithm is that it avoids computationally expensive graph isomorphism tests and overcomes the space limitation of the static expansion tree (SET) which makes it enable to find large motifs. In this algorithm, the embeddings corresponding to a child node of the expansion tree are obtained from the embeddings of a parent node, either by adding a vertex or by adding an edge. This process does not involve any graph isomorphism check. The time complexity of vertex addition and edge addition are O(n) and O(1), respectively. The growth of a dynamic expansion tree (DET) depends on the availability of patterns in the target network. Pruning of branches in the DET significantly reduces the space requirement of the SET. The proposed algorithm has been tested on a protein–protein interaction network obtained from the MINT database. The proposed algorithm is able to identify large network motifs faster than most of the existing motif finding algorithms.

Motif discovery in biological network using expansion tree

2018 ◽  
Vol 16 (06) ◽  
pp. 1850024 ◽  
Author(s):  
Sabyasachi Patra ◽  
Anjali Mohapatra
Keyword(s):  
Complex Networks ◽  
Protein Interaction ◽  
Motif Discovery ◽  
Statistical Significance ◽  
Network Motif ◽  
Graph Isomorphism ◽  
Building Blocks ◽  
Network Motifs ◽  
Topological Features ◽  
Scalable Network

Networks are powerful representation of topological features in biological systems like protein interaction and gene regulation. In order to understand the design principles of such complex networks, the concept of network motifs emerged. Network motifs are recurrent patterns with statistical significance that can be seen as basic building blocks of complex networks. Identification of network motifs leads to many important applications, such as understanding the modularity and the large-scale structure of biological networks, classification of networks into super-families, protein function annotation, etc. However, identification of network motifs is challenging as it involves graph isomorphism which is computationally hard. Though this problem has been studied extensively in the literature using different computational approaches, we are far from satisfactory results. Motivated by the challenges involved in this field, an efficient and scalable network Motif Discovery algorithm based on Expansion Tree (MODET) is proposed. Pattern growth approach is used in this proposed motif-centric algorithm. Each node of the expansion tree represents a non-isomorphic pattern. The embeddings corresponding to a child node of the expansion tree are obtained from the embeddings of the parent node through vertex addition and edge addition. Further, the proposed algorithm does not involve any graph isomorphism check and the time complexities of these processes are [Formula: see text] and [Formula: see text], respectively. The proposed algorithm has been tested on Protein–Protein Interaction (PPI) network obtained from the MINT database. The computational efficiency of the proposed algorithm outperforms most of the existing network motif discovery algorithms.

scholarly journals Discovery of Large Disjoint Motif in Biological Network using Dynamic Expansion Tree

2018 ◽  
Author(s):  
Sabyasachi Patra ◽  
Anjali Mohapatra
Keyword(s):  
Biological Networks ◽  
Time Complexity ◽  
Motif Discovery ◽  
Large Scale ◽  
Graph Isomorphism ◽  
Network Motifs ◽  
Protein Protein Interaction ◽  
Target Network ◽  
Discovery Algorithms

AbstractNetwork motifs play an important role in structural analysis of biological networks. Identification of such network motifs leads to many important applications, such as: understanding the modularity and the large-scale structure of biological networks, classification of networks into super-families etc. However, identification of network motifs is challenging as it involved graph isomorphism which is computationally hard problem. Though this problem has been studied extensively in the literature using different computational approaches, we are far from encouraging results. Motivated by the challenges involved in this field we have proposed an efficient and scalable Motif discovery algorithm using a Dynamic Expansion Tree (MDET). In this algorithm embeddings corresponding to child node of expansion tree are obtained from the embeddings of parent node, either by adding a vertex with time complexity O(n) or by adding an edge with time complexity O(1) without involving any isomorphic check. The growth of Dynamic Expansion Tree (DET) depends on availability of patterns in the target network. DET reduces space complexity significantly and the memory limitation of static expansion tree can overcome. The proposed algorithm has been tested on Protein Protein Interaction (PPI) network obtained from MINT database. It is able to identify large motifs faster than most of the existing motif discovery algorithms.

scholarly journals Community Detection in Large-Scale Bipartite Biological Networks

2021 ◽  
Vol 12 ◽  
Author(s):  
Genís Calderer ◽  
Marieke L. Kuijjer
Keyword(s):  
Biological Networks ◽  
Large Scale ◽  
Interaction Network ◽  
Gene Interaction ◽  
Community Structures ◽  
Gene Interaction Network ◽  
Structure Detection ◽  
Wide Range ◽  
Disease Associations ◽  
Or Gene

Networks are useful tools to represent and analyze interactions on a large, or genome-wide scale and have therefore been widely used in biology. Many biological networks—such as those that represent regulatory interactions, drug-gene, or gene-disease associations—are of a bipartite nature, meaning they consist of two different types of nodes, with connections only forming between the different node sets. Analysis of such networks requires methodologies that are specifically designed to handle their bipartite nature. Community structure detection is a method used to identify clusters of nodes in a network. This approach is especially helpful in large-scale biological network analysis, as it can find structure in networks that often resemble a “hairball” of interactions in visualizations. Often, the communities identified in biological networks are enriched for specific biological processes and thus allow one to assign drugs, regulatory molecules, or diseases to such processes. In addition, comparison of community structures between different biological conditions can help to identify how network rewiring may lead to tissue development or disease, for example. In this mini review, we give a theoretical basis of different methods that can be applied to detect communities in bipartite biological networks. We introduce and discuss different scores that can be used to assess the quality of these community structures. We then apply a wide range of methods to a drug-gene interaction network to highlight the strengths and weaknesses of these methods in their application to large-scale, bipartite biological networks.

scholarly journals Neural Differentiation Dynamics Controlled by Multiple Feedback Loops in a Comprehensive Molecular Interaction Network

Processes ◽  
2020 ◽  
Vol 8 (2) ◽  
pp. 166
Author(s):  
Tsuyoshi Iwasaki ◽  
Ryo Takiguchi ◽  
Takumi Hiraiwa ◽  
Takahiro G. Yamada ◽  
Kazuto Yamazaki ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Neural Differentiation ◽  
Large Scale ◽  
Model Simulation ◽  
Interaction Network ◽  
Feedback Loops ◽  
Characteristic Change ◽  
Large Network ◽  
Large Scale Network ◽  
Scale Network

Mathematical model simulation is a useful method for understanding the complex behavior of a living system. The construction of mathematical models using comprehensive information is one of the techniques of model construction. Such a comprehensive knowledge-based network tends to become a large-scale network. As a result, the variation of analyses is limited to a particular kind of analysis because of the size and complexity of the model. To analyze a large-scale regulatory network of neural differentiation, we propose a contractive method that preserves the dynamic behavior of a large network. The method consists of the following two steps: comprehensive network building and network reduction. The reduction phase can extract network loop structures from a large-scale regulatory network, and the subnetworks were combined to preserve the dynamics of the original large-scale network. We confirmed that the extracted loop combination reproduced the known dynamics of HES1 and ASCL1 before and after differentiation, including oscillation and equilibrium of their concentrations. The model also reproduced the effects of the overexpression and knockdown of the Id2 gene. Our model suggests that the characteristic change in HES1 and ASCL1 expression in the large-scale regulatory network is controlled by a combination of four feedback loops, including a large loop, which has not been focused on. The model extracted by our method has the potential to reveal the critical mechanisms of neural differentiation. The method is applicable to other biological events.

NMDB: NETWORK MOTIF DATABASE ENVISAGED AND EXPLICATED FROM HUMAN DISEASE SPECIFIC PATHWAYS

2014 ◽  
Vol 22 (01) ◽  
pp. 89-100 ◽  
Author(s):  
ABHAY PRATAP ◽  
SETU TALIYAN ◽  
TIRATHA RAJ SINGH
Keyword(s):  
Biological Networks ◽  
Human Disease ◽  
Biological Network ◽  
Metabolic Diseases ◽  
Network Motif ◽  
Network Motifs ◽  
Efficient Detection ◽  
Single Input ◽  
Motif Database ◽  
Disease Specific

The study of network motifs for large number of networks can aid us to resolve the functions of complex biological networks. In biology, network motifs that reappear within a network more often than expected in random networks include negative autoregulation, positive autoregulation, single-input modules, feedforward loops, dense overlapping regulons and feedback loops. These network motifs have their different dynamical functions. In this study, our main objective is to examine the enrichment of network motifs in different biological networks of human disease specific pathways. We characterize biological network motifs as biologically significant sub-graphs. We used computational and statistical criteria for efficient detection of biological network motifs, and introduced several estimation measures. Pathways of cardiovascular, cancer, infectious, repair, endocrine and metabolic diseases, were used for identifying and interlinking the relation between nodes. 3–8 sub-graph size network motifs were generated. Network Motif Database was then developed using PHP and MySQL. Results showed that there is an abundance of autoregulation, feedforward loops, single-input modules, dense overlapping regulons and other putative regulatory motifs in all the diseases included in this study. It is believed that the database will assist molecular and system biologists, biotechnologists, and other scientific community to encounter biologically meaningful information. Network Motif Database is freely available for academic and research purpose at: http://www.bioinfoindia.org/nmdb .

scholarly journals Algorithms for protein interaction networks

2005 ◽  
Vol 33 (3) ◽  
pp. 530-534 ◽  
Author(s):  
M. Lappe ◽  
L. Holm
Keyword(s):  
Protein Interactions ◽  
Biological Networks ◽  
Protein Function ◽  
Large Scale ◽  
Sequence Similarity ◽  
Functional Characterization ◽  
Interaction Networks ◽  
Computational Techniques ◽  
Interaction Patterns ◽  
Main Challenge

The functional characterization of all genes and their gene products is the main challenge of the postgenomic era. Recent experimental and computational techniques have enabled the study of interactions among all proteins on a large scale. In this paper, approaches will be presented to exploit interaction information for the inference of protein structure, function, signalling pathways and ultimately entire interactomes. Interaction networks can be modelled as graphs, showing the operation of gene function in terms of protein interactions. Since the architecture of biological networks differs distinctly from random networks, these functional maps contain a signal that can be used for predictive purposes. Protein function and structure can be predicted by matching interaction patterns, without the requirement of sequence similarity. Moving on to a higher level definition of protein function, the question arises how to decompose complex networks into meaningful subsets. An algorithm will be demonstrated, which extracts whole signal-transduction pathways from noisy graphs derived from text-mining the biological literature. Finally, an algorithmic strategy is formulated that enables the proteomics community to build a reliable scaffold of the interactome in a fraction of the time compared with uncoordinated efforts.

scholarly journals An Enhancement of Grami Based on Threshold Policy for Pattern Big Graphs

2020 ◽  
Vol 9 (3) ◽  
pp. 2943-2949
Keyword(s):  
Biological Networks ◽  
Interconnection Networks ◽  
Large Scale ◽  
Pattern Mining ◽  
Constraint Satisfaction Problem ◽  
Interaction Network ◽  
Frequent Subgraph Mining ◽  
Threshold Policy ◽  
Subgraph Mining ◽  
Frequent Subgraph

Pattern Mining is the key mechanism to manage large scale data element. Frequent subgraph mining (FSM) considers isomorphism which is a subprocess of pattern mining is a well-studied problem in the data mining. Graphs are considered as a standard structure in many domains such as protein-protein interaction network in biological networks, wired or wireless interconnection networks, web data, etc. FSM is the task of finding all frequent subgraphs from a given database i.e. a single big graph or database of many graphs, whose support is greater than the given threshold value. Many databases consider small graphs for solving complex problems. The classification of graph depends upon the application requirement. A good mining architecture may prevent a lot of memory and time. This paper follows the Grami structure for the analysis of frequent subgraph mining and also introduces the 20% threshold policy for the enhancement of the directed pattern graphs. The constraint satisfaction problem (CSP) has been discussed and analyzed using the Grami approach. The proposed model is compared to Grami on twitter dataset based on the evaluation of time and memory consumed. The proposed algorithm shows an improvement of 3-4 % for both the parameters. The results show that the performance of Grami approach has been improved which shows a 6.6% reduction in time and 21% improvement in memory consumption using the proposed approach.

scholarly journals Large-scale identification of human protein function using topological features of interaction network

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Zhanchao Li ◽  
Zhiqing Liu ◽  
Wenqian Zhong ◽  
Menghua Huang ◽  
Na Wu ◽  
...  
Keyword(s):  
Protein Function ◽  
Large Scale ◽  
Interaction Network ◽  
Human Protein ◽  
Topological Features

scholarly journals Nonlinear delay differential equations and their application to modeling biological network motifs

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
David S. Glass ◽  
Xiaofan Jin ◽  
Ingmar H. Riedel-Kruse
Keyword(s):  
Differential Equation ◽  
Biological Networks ◽  
Network Motif ◽  
Network Motifs ◽  
Ode Models ◽  
Regulatory Systems ◽  
Nonlinear Delay Differential Equations ◽  
Cell Signaling Networks ◽  
Analytical Relations ◽  
Delay Differential

AbstractBiological regulatory systems, such as cell signaling networks, nervous systems and ecological webs, consist of complex dynamical interactions among many components. Network motif models focus on small sub-networks to provide quantitative insight into overall behavior. However, such models often overlook time delays either inherent to biological processes or associated with multi-step interactions. Here we systematically examine explicit-delay versions of the most common network motifs via delay differential equation (DDE) models, both analytically and numerically. We find many broadly applicable results, including parameter reduction versus canonical ordinary differential equation (ODE) models, analytical relations for converting between ODE and DDE models, criteria for when delays may be ignored, a complete phase space for autoregulation, universal behaviors of feedforward loops, a unified Hill-function logic framework, and conditions for oscillations and chaos. We conclude that explicit-delay modeling simplifies the phenomenology of many biological networks and may aid in discovering new functional motifs.

scholarly journals Nonlinear delay differential equations and their application to modeling biological network motifs

2020 ◽  
Author(s):  
David S. Glass ◽  
Xiaofan Jin ◽  
Ingmar H. Riedel-Kruse
Keyword(s):  
Differential Equations ◽  
Biological Networks ◽  
Delay Differential Equations ◽  
Network Motif ◽  
Network Motifs ◽  
Mathematical Form ◽  
Unified Framework ◽  
Regulatory Systems ◽  
Nonlinear Delay Differential Equations ◽  
Delay Differential

AbstractBiological regulatory systems, such as transcription factor or kinase networks, nervous systems and ecological webs, consist of complex dynamical interactions among many components. “Network motif” models focus on small sub-networks to provide quantitative insight into overall behavior. However, conventional network motif models often ignore time delays either inherent to biological processes or associated with multi-step interactions. Here we systematically examine explicit-delay versions of the most common network motifs via delay differential equations (DDEs), both analytically and numerically. We find many broadly applicable results, such as the reduction in number of parameters compared to canonical descriptions via ordinary differential equations (ODE), criteria for when delays may be ignored, a complete phase space for autoregulation, explicit dependence of feedforward loops on a difference of delays, a unified framework for Hill-function logic, and conditions for oscillations and chaos. We emphasize relevance to biological function throughout our analysis, summarize key points in non-mathematical form, and conclude that explicit-delay modeling simplifies the phenomenological understanding of many biological networks and may aid in discovering new functional motifs.

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