PPI network
A New Method of Constructing a Weighted PPI Network
... PPI network can be expressed as G = ( , , ) v e w where v stands for a protein node, e stands for an interaction between a couple of proteins, and w indicates the weight of ...weighted network can ...
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A Study And Analysis Of Biclustering Algorithms To Identify Ppi Network And Significant Enrichments Of Genes In Biclusters Based On Gene Ontology And Kegg Pathway Database
... (PPI) network for the identified biclusters and finally the extractions of significant enrichments based on KEGG and ...the PPI network for the significant genes present in each biclust er of ...
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Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology
... on network density [32]; the MCL method, based on random walk [33]; the COACH method, based on core-attachment structure [34]; and clustering by cliques ...in PPI network is a subgraph in which each ...
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Original Article Protein-protein interaction (PPI) network and significant gene analysis of breast cancer
... Path PPI interaction data to construct the signal transduction net- work and transcriptional regulatory ...regulatory network con- tained 35 DEGs and 37 interaction relation- ...transduction network ...
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Systematic analysis of protein interaction network associated with azoospermia
... Examination of the key nodes identified in our PPI network suggested proteins crebbp and bcar1, which have never been associated with azoospermia. crebbp is responsible for handling Gap 1 (G1) arrest during ...
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An integrated analysis for long noncoding RNAs and microRNAs with the mediated competing endogenous RNA network in papillary renal cell carcinoma
... This PPI network showed 122 nodes and 962 interactions. The most significant hub genes were nuclear receptor subfamily 4 group A member 2 (NR4A2), dachshund family transcription factor 1 (DACH1), glypican 5 ...
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Decomposing PPI networks for complex discovery
... PPI network into several smaller networks such that interactions within each smaller network are contex- tually ...decompose PPI networks because a protein complex can be formed only if its ...
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Revealing protein functions based on relationships of interacting proteins and GO terms
... Functional relationship between interacting proteins As reported, many proteins play functional roles that are different from their neighbors in the PPI network. For example, a protein annotated with terms: ...
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iTRAQ-based quantitative proteomic analysis provides insight for molecular mechanism of neuroticism
... Similarly, among patients with lung cancer, neuroti- cism increases the risk of depression and anxiety, and is particularly associated with higher levels of anxiety in female patients [47]. Our study found that the ...
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Design principles for cancer therapy guided by changes in complexity of protein-protein interaction networks
... particular network. The protein-protein inter- action (PPI) network for AML based on KEGGgraph ...The network breaks into two “components” but the inhibition does not result in a complete ...
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Unequal evolutionary conservation of human protein interactions in interologous networks
... human PPI network are more conserved than the lower degree proteins, and the proportion of proteins conserved decreases with evolutionary ...a PPI dataset, it is important to understand whether all ...
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Identify differential gene expressions in fatty infiltration process in rotator cuff
... Till now, the key genes and pathway involved in the fatty infiltration of rotator cuff tear still unclear. Ren et al. identified differentially expressed genes and signaling pathways involved in rotator cuff tear through ...
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Identification of hub genes and outcome in colon cancer based on bioinformatics analysis
... (PPI) network construction, sub-modules analysis, overall survival (OS) analysis, genes correlation analysis, and construction of non-coding RNA-related regulatory network were used for analyzing ...
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Systems biology network-based discovery of a small molecule activator BL-AD008 targeting AMPK/ZIPK and inducing apoptosis in cervical cancer
... (PPI) network and predicted apoptosis-related protein connections by the Naïve Bayesian ...biology network to identify some key apoptotic kinase targets AMPK and ZIPK; thus providing a dual-target ...
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Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis
... the PPI network for gene set G1 showed that ribosomal protein L3 (RPL3) gene could interact with heat shock protein 90 kDa alpha, class A member 1 ...integrated network for gene set G2, ...
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Analyses of gene expression profiles in the rat dorsal horn of the spinal cord using RNA sequencing in chronic constriction injury rats
... PPI network analysis showed that Cd68, C1qc, C1qa, Laptm5, and Fcgr3a were crucial nodes with high con- nectivity degrees. Laptm5 and Fcgr3a which have previ- ously been linked to immune and ...
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Original Article Screening key genes associated with congenital heart defects in Down syndrome based on differential expression network
... 24]. Network-based approaches have been developed to extract informative genes relying on biomolecular networks ...(PPI) network and gene regula- tory network), rather than individual ...
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Assortativity of aging key players in the dynamical networks
... the network across ...the network, we analyzed the property of assortativity as proposed by recent ...in PPI network is a measure to quantify the tendency of proteins to communicate with other ...
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Integrated bioinformatic analysis unveils significant genes and pathways in the pathogenesis of supratentorial primitive neuroectodermal tumor
... In the present study, we downloaded a gene expres- sion profile from publicly available database and carried out systematic bioinformatics analysis. Differentially expressed genes (DEGs) were screened out in primary ...
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Original Article The PPAR signaling pathway as a potential biomarker for the diagnosis of breast cancer
... (PPI) network were built in the training dataset (GSE42568) using the twenty-one differentially expressed genes (DEGs) which were annotated into the PPAR signaling ...A PPI analysis showed that the ...
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