Transcriptomics to Metabolomics

Author(s):  
Ankush Bansal ◽  
Pulkit Anupam Srivastava

A lot of omics data is generated in a recent decade which flooded the internet with transcriptomic, genomics, proteomics and metabolomics data. A number of software, tools, and web-servers have developed to analyze the big data omics. This review integrates the various methods that have been employed over the years to interpret the gene regulatory and metabolic networks. It illustrates random networks, scale-free networks, small world network, bipartite networks and other topological analysis which fits in biological networks. Transcriptome to metabolome network is of interest because of key enzymes identification and regulatory hub genes prediction. It also provides an insight into the understanding of omics technologies, generation of data and impact of in-silico analysis on the scientific community.

Biotechnology ◽  
2019 ◽  
pp. 361-379
Author(s):  
Ankush Bansal ◽  
Pulkit Anupam Srivastava

A lot of omics data is generated in a recent decade which flooded the internet with transcriptomic, genomics, proteomics and metabolomics data. A number of software, tools, and web-servers have developed to analyze the big data omics. This review integrates the various methods that have been employed over the years to interpret the gene regulatory and metabolic networks. It illustrates random networks, scale-free networks, small world network, bipartite networks and other topological analysis which fits in biological networks. Transcriptome to metabolome network is of interest because of key enzymes identification and regulatory hub genes prediction. It also provides an insight into the understanding of omics technologies, generation of data and impact of in-silico analysis on the scientific community.


2020 ◽  
Vol 17 (163) ◽  
pp. 20190845
Author(s):  
Pablo Villegas ◽  
Miguel A. Muñoz ◽  
Juan A. Bonachela

Biological networks exhibit intricate architectures deemed to be crucial for their functionality. In particular, gene regulatory networks, which play a key role in information processing in the cell, display non-trivial architectural features such as scale-free degree distributions, high modularity and low average distance between connected genes. Such networks result from complex evolutionary and adaptive processes difficult to track down empirically. On the other hand, there exists detailed information on the developmental (or evolutionary) stages of open-software networks that result from self-organized growth across versions. Here, we study the evolution of the Debian GNU/Linux software network, focusing on the changes of key structural and statistical features over time. Our results show that evolution has led to a network structure in which the out-degree distribution is scale-free and the in-degree distribution is a stretched exponential. In addition, while modularity, directionality of information flow, and average distance between elements grew, vulnerability decreased over time. These features resemble closely those currently shown by gene regulatory networks, suggesting the existence of common adaptive pathways for the architectural design of information-processing networks. Differences in other hierarchical aspects point to system-specific solutions to similar evolutionary challenges.


10.1068/b306 ◽  
2004 ◽  
Vol 31 (1) ◽  
pp. 151-162 ◽  
Author(s):  
Bin Jiang ◽  
Christophe Claramunt

The authors propose a topological analysis of large urban street networks based on a computational and functional graph representation. This representation gives a functional view in which vertices represent named streets and edges represent street intersections. A range of graph measures, including street connectivity, average path length, and clustering coefficient, are computed for structural analysis. In order to characterise different clustering degrees of streets in a street network they generalise the clustering coefficient to a k-clustering coefficient that takes into account k neighbours. Based on validations applied to three cities, the authors show that large urban street networks form small-world networks but exhibit no scale-free property.


Entropy ◽  
2020 ◽  
Vol 22 (6) ◽  
pp. 622 ◽  
Author(s):  
Michael Nosonovsky ◽  
Prosun Roy

Scaling and dimensional analysis is applied to networks that describe various physical systems. Some of these networks possess fractal, scale-free, and small-world properties. The amount of information contained in a network is found by calculating its Shannon entropy. First, we consider networks arising from granular and colloidal systems (small colloidal and droplet clusters) due to pairwise interaction between the particles. Many networks found in colloidal science possess self-organizing properties due to the effect of percolation and/or self-organized criticality. Then, we discuss the allometric laws in branching vascular networks, artificial neural networks, cortical neural networks, as well as immune networks, which serve as a source of inspiration for both surface engineering and information technology. Scaling relationships in complex networks of neurons, which are organized in the neocortex in a hierarchical manner, suggest that the characteristic time constant is independent of brain size when interspecies comparison is conducted. The information content, scaling, dimensional, and topological properties of these networks are discussed.


2014 ◽  
Vol 1 (3) ◽  
pp. 346-356 ◽  
Author(s):  
Jianxi Gao ◽  
Daqing Li ◽  
Shlomo Havlin

Abstract Network science has attracted much attention in recent years due to its interdisciplinary applications. We witnessed the revolution of network science in 1998 and 1999 started with small-world and scale-free networks having now thousands of high-profile publications, and it seems that since 2010 studies of ‘network of networks’ (NON), sometimes called multilayer networks or multiplex, have attracted more and more attention. The analytic framework for NON yields a novel percolation law for n interdependent networks that shows that percolation theory of single networks studied extensively in physics and mathematics in the last 50 years is a specific limit of the rich and very different general case of n coupled networks. Since then, properties and dynamics of interdependent and interconnected networks have been studied extensively, and scientists are finding many interesting results and discovering many surprising phenomena. Because most natural and engineered systems are composed of multiple subsystems and layers of connectivity, it is important to consider these features in order to improve our understanding of such complex systems. Now the study of NON has become one of the important directions in network science. In this paper, we review recent studies on the new emerging area—NON. Due to the fast growth of this field, there are many definitions of different types of NON, such as interdependent networks, interconnected networks, multilayered networks, multiplex networks and many others. There exist many datasets that can be represented as NON, such as network of different transportation networks including flight networks, railway networks and road networks, network of ecological networks including species interacting networks and food webs, network of biological networks including gene regulation network, metabolic network and protein–protein interacting network, network of social networks and so on. Among them, many interdependent networks including critical infrastructures are embedded in space, introducing spatial constraints. Thus, we also review the progress on study of spatially embedded networks. As a result of spatial constraints, such interdependent networks exhibit extreme vulnerabilities compared with their non-embedded counterparts. Such studies help us to understand, realize and hopefully mitigate the increasing risk in NON.


2021 ◽  
Vol 9 ◽  
Author(s):  
Xiaomin Wang ◽  
Fei Ma ◽  
Bing Yao

Complex networks have become a powerful tool to describe the structure and evolution in a large quantity of real networks in the past few years, such as friendship networks, metabolic networks, protein–protein interaction networks, and software networks. While a variety of complex networks have been published, dense networks sharing remarkable structural properties, such as the scale-free feature, are seldom reported. Here, our goal is to construct a class of dense networks. Then, we discover that our networks follow the mixture degree distribution; that is, there is a critical point above which the cumulative degree distribution has a power-law form and below which the exponential distribution is observed. Next, we also prove the networks proposed to show the small-world property. Finally, we study random walks on our networks with a trap fixed at a vertex with the highest degree and find that the closed form for the mean first-passage time increases logarithmically with the number of vertices of our networks.


2019 ◽  
Author(s):  
Kumar Selvarajoo

AbstractNon-linear Kuramoto model has been used to study synchronized or sync behavior in numerous fields, however, its application in biology is scare. Here, I introduce the basic model and provide examples where large scale small-world or scale-free networks are crucial for spontaneous sync even for low coupling strength. This information was next checked for relevance in living systems where it is now well-known that biological networks are scale-free. Our recent transcriptome-wide data analysis of Saccharomyces cerevisiae biofilm showed that low to middle expressed genes are key for scale invariance in biology. Together, the current data indicate that biological network connectivity structure with low coupling strength, or expression levels, is sufficient for sync behavior. For biofilm regulation, it may, therefore, be necessary to investigate large scale low expression genes rather than small scale high expression genes.


PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0247191
Author(s):  
Bingyong Xu ◽  
Hong Su ◽  
Ruya Wang ◽  
Yixiao Wang ◽  
Weidong Zhang

Whether osteoarthritis (OA) is a systemic metabolic disorder remains controversial. The aim of this study was to investigate the metabolic characteristics between plasma and knee joint fluid (JF) of patients with advanced OA using a differential correlation metabolic (DCM) networks approach. Plasma and JF were collected during the joint replacement surgery of patients with knee OA. The biological samples were pretreated with standard procedures for metabolite analysis. The metabolic profiling was conducted by means of liquid mass spectrometry coupled with a AbsoluteIDQ kit. A DCM network approach was adopted for analyzing the metabolomics data between the plasma and JF. The variation in the correlation of the pairwise metabolites was quantified across the plasma and JF samples, and networks analysis was used to characterize the difference in the correlations of the metabolites from the two sample types. Core metabolites that played an important role in the DCM networks were identified via topological analysis. One hundred advanced OA patients (50 men and 50 women) were included in this study, with an average age of 65.0 ± 7.6 years (65.6 ± 7.1 years for females and 64.4 ± 8.1 years for males) and a mean BMI of 32.6 ± 5.8 kg/m2 (33.4 ± 6.3 kg/m2 for females and 31.7 ± 5.3 kg/m2 for males). Age and BMI matched between the male and female groups. One hundred and forty-five nodes, 567 edges, and 131 nodes, 407 edges were found in the DCM networks (p < 0.05) of the female and male groups, respectively. Six metabolites in the female group and 5 metabolites in the male group were identified as key nodes in the network. There was a significant difference in the differential correlation metabolism networks of plasma and JF that may be related to local joint metabolism. Focusing on these key metabolites may help uncover the pathogenesis of knee OA. In addition, the differential metabolic correlation between plasma and JF mostly overlapped, indicating that these common correlations of pairwise metabolites may be a reflection of systemic characteristics of JF and that most significant correlation variations were just a result of "housekeeping” biological reactions.


2014 ◽  
Vol 894 ◽  
pp. 280-283
Author(s):  
Bin Yang ◽  
Chuan Zhu Liao ◽  
Ming Yan Jiang ◽  
Dong Feng Yuan

Stochastic dynamics and delayed time of biochemical reactions play an important role in the biological networks such as gene regulatory and metabolic networks. This paper presents a new model, called additive reaction model (ARM), to capture the stochastic dynamical and delayed behavior. The new evolutionary strategy is used to search the optimal biochemical model, in which genetic algorithm (GA) and particle swarm optimization (PSO) are employed to evolve the architecture and parameters of biochemical reactions, respectively. The results reveal that the delayed biochemical reaction modeling problems could be solved effectively and efficiently using our proposed new model and new evolutionary strategy.


Cancers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 393
Author(s):  
Derek van Tilborg ◽  
Edoardo Saccenti

One of the major hallmarks of cancer is the derailment of a cell’s metabolism. The multifaceted nature of cancer and different cancer types is transduced by both its transcriptomic and metabolomic landscapes. In this study, we re-purposed the publicly available transcriptomic and metabolomics data of eight cancer types (breast, lung, gastric, renal, liver, colorectal, prostate, and multiple myeloma) to find and investigate differences and commonalities on a pathway level among different cancer types. Topological analysis of inferred graphical Gaussian association networks showed that cancer was strongly defined in genetic networks, but not in metabolic networks. Using different statistical approaches to find significant differences between cancer and control cases, we highlighted the difficulties of high-level data-merging and in using statistical association networks. Cancer transcriptomics and metabolomics and landscapes were characterized by changed macro-molecule production, however, only major metabolic deregulations with highly impacted pathways were found in liver cancer. Cell cycle was enriched in breast, liver, and colorectal cancer, while breast and lung cancer were distinguished by highly enriched oncogene signaling pathways. A strong inflammatory response was observed in lung cancer and, to some extent, renal cancer. This study highlights the necessity of combining different omics levels to obtain a better description of cancer characteristics.


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