Identification of key regulators in Prostate cancer from gene expression datasets of patients

Mangangcha, Irengbam Rocky; Malik, Md. Zubbair; Küçük, Ömer; Ali, Shakir

doi:10.1101/643643

Cited by 4 publications

(4 citation statements)

References 104 publications

(107 reference statements)

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“…This implies that triangular motifs is correlated with signalling network of cancer. Indeed, triangular network motifs are abundantly found in many cancer studies using network biology approach [54][55][56][57][58][59][60]. Our study thus highlights a close relation between thermodynamic cost-precision (thermodynamic uncertainty relation), triangular motifs and cancer.…”

Section: Discussionsupporting

confidence: 61%

Thermodynamic Uncertainty Relation in the interlinked cascade of RabGTPases

Chanu¹,

Singh²

2022

Preprint

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We model the well-known interlinked cascade of Rab GTPases found in eukaryotic cells by using a network of Markov states to investigate if the universal Thermodynamic Uncertainty Relation (TUR) is obeyed in such non-equilibrium system. First, we prove numerically the TUR in both single species model and double species interlinked model. Moreover, our TUR results show that when two Rab GTPase proteins are interlinked, the thermodynamic cost and hence precision is greatly enhanced as compared to single species switching. This implies that at far from equilibrium, the proteins tries to optimise the precision of their performance of biological processes by forming interlinks in the cascade. Again,our TUR results imply that the interlinked cascade (or oscillator) can achieve a range of tunable rate constants (or frequencies) which suggests a means of maintaining its robustness. Lastly, we highlight a close relation between thermodynamic cost-precision, triangular motifs and cancer biology.

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Section: Discussionsupporting

confidence: 61%

Thermodynamic Uncertainty Relation in the interlinked cascade of RabGTPases

Chanu¹,

Singh²

2022

Preprint

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“…The PPI study of the identified protein sets and the protein community finding by in silico network analysis identified a set of key regulator molecules [42][43][44][45] Upon TXR treatment, the C9, AAG and catalase abundance were decreased almost to the basal levels without significant alteration in CRP, a non-specific indicator of inflammation. High aldehyde dehydrogenase (ALDH) activity has been reported in osteoarthritis patients'…”

Section: Discussionmentioning

confidence: 99%

Troxerutin acts on complement mediated inflammation to ameliorate arthritic symptoms in rats

Sahu

Bishwal

Malik

et al. 2020

Preprint

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Troxerutin (TXR), a phytochemical reported to possess anti-inflammatory and hepato-protective effects. In this study, we aimed to exploit anti-arthritic properties of TXR using an adjuvant induced arthritic (AIA) rat model. AIA induced rats showed highest arthritis score at disease onset and by oral administration of TXR (50, 100, 200 mg/kg body weight), reduced to basal level in a dose dependent manner. Isobaric tag for relative and absolute quantitative (iTRAQ) proteomics tool was employed to identify deregulated joint homogenate proteins in AIA and TXR treated rats to decipher probable mechanism of the TXR action in arthritis. iTRAQ analysis identified a set of 434 joint homogenate proteins with 65 deregulated proteins (log2 case/control ≥1.5) in AIA. Expressions of a set of important proteins (AAT, T-kininogen, vimentin, desmin, nucleophosmin) that could classify AIA from healthy were validated using Western blot analysis. Western blot data corroborated proteomics findings. In silico protein-protein interaction study of joint homogenate proteome revealed that complement component 9, the major building blocks of the membrane attack complex (MAC) responsible for sterile inflammation, gets perturbed in AIA. Our dosimetry study suggests that a TXR dose of 200 mg/kg body weight for 15 days is sufficient to bring the arthritis score to basal levels in AIA rats. We have shown the importance of TXR as an anti-arthritis agent in AIA model and after additional investigation its arthritis ameliorating properties could be exploited for clinical usability.

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“…These experiments involve eliminating the most in uential nodes in the network and studying the resulting reorganized networks. [36,37]. Furthermore, in uential nodes have been identi ed using community detection-based methods [38,39].…”

Section: Related Workmentioning

confidence: 99%

InfVIKOR: A hybrid Decision-Making computational approach to identify influential nodes in complex networks

Singh,

Patel,

Sharma

et al. 2024

Preprint

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Identifying influential nodes in complex networks remains a significant challenge in network analysis. In this direction, one attractive challenge is to characterize the spreading capabilities of nodes, which could serve as potential regulators of the network. While node centrality methods have been widely used for identifying such nodes, they are often tailored to specific problems. In this research work, a new method InfVIKOR is proposed aimed at accurately identifying influential nodes and addressing bias inherent in single-measure evaluations. This method utilizes a Multi-Criteria Decision Making (MCDM) approach called VIKOR, which integrates multiple parameters to effectively identify influential nodes. The method uses the centrality measure as a criterion with proper optimization method to construct group utility function of the complex network, and then quick sort algorithm is applied to rank the nodes according to their influence score derived from the group utility measure. InfVIKOR prioritizes influential nodes to achieve a balanced combination of efficacy and efficiency. To evaluate the effectiveness of the method, the Susceptible-Infected (SI) model is employed to simulate communication propagation across six real-world networks. The experimental findings underscore the accuracy and efficacy of the proposed method. Further, this method can be used in any hierarchical scale free networks.

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Identification of key regulators in Prostate cancer from gene expression datasets of patients

Cited by 4 publications

References 104 publications

Thermodynamic Uncertainty Relation in the interlinked cascade of RabGTPases

Thermodynamic Uncertainty Relation in the interlinked cascade of RabGTPases

Troxerutin acts on complement mediated inflammation to ameliorate arthritic symptoms in rats

InfVIKOR: A hybrid Decision-Making computational approach to identify influential nodes in complex networks

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