Global Alignment of PPI Networks

2020 ◽  
pp. 3-25
Author(s):  
Cesim Erten
Keyword(s):  
Global Alignment ◽  
Ppi Networks

scholarly journals Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Wenhong Tian ◽  
Nagiza F. Samatova
Keyword(s):  
Protein Interaction ◽  
Computational Cost ◽  
Network Alignment ◽  
Connected Components ◽  
Global Alignment ◽  
E Coli ◽  
Ppi Networks ◽  
Specificity And Sensitivity ◽  
Global Mapping ◽  
Interaction Regions

A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach based on a precompiled list of homologs identified by KO terms. Applying this approach toS. cerevisiae(yeast) andD. melanogaster(fly),E. coliK12 andS. typhimurium,E. coliK12 andC. crescenttus, we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily.

scholarly journals A novel algorithm for alignment of multiple PPI networks based on simulated annealing

BMC Genomics ◽  
2019 ◽  
Vol 20 (S13) ◽  
Author(s):  
Jialu Hu ◽  
Junhao He ◽  
Jing Li ◽  
Yiqun Gao ◽  
Yan Zheng ◽  
...  
Keyword(s):  
Protein Function ◽  
Global Alignment ◽  
Alignment Algorithm ◽  
Algorithm Performance ◽  
Ppi Networks ◽  
Annotation Data ◽  
Increasing Demand ◽  
Almost All ◽  
Functional Analyses

AbstractProteins play essential roles in almost all life processes. The prediction of protein function is of significance for the understanding of molecular function and evolution. Network alignment provides a fast and effective framework to automatically identify functionally conserved proteins in a systematic way. However, due to the fast growing genomic data, interactions and annotation data, there is an increasing demand for more accurate and efficient tools to deal with multiple PPI networks. Here, we present a novel global alignment algorithm NetCoffee2 based on graph feature vectors to discover functionally conserved proteins and predict function for unknown proteins. To test the algorithm performance, NetCoffee2 and three other notable algorithms were applied on eight real biological datasets. Functional analyses were performed to evaluate the biological quality of these alignments. Results show that NetCoffee2 is superior to existing algorithms IsoRankN, NetCoffee and multiMAGNA++ in terms of both coverage and consistency. The binary and source code are freely available under the GNU GPL v3 license at https://github.com/screamer/NetCoffee2.

scholarly journals LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules

BMC Genomics ◽  
2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Sawal Maskey ◽  
Young-Rae Cho
Keyword(s):  
Computational Cost ◽  
Network Alignment ◽  
System Level ◽  
Local Network ◽  
Local Alignment ◽  
Global Alignment ◽  
Alignment Algorithm ◽  
Interaction Patterns ◽  
Ppi Networks ◽  
Alignment Algorithms

Abstract Background Cross-species analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved interaction patterns. Identifying such conserved substructures between PPI networks of different species increases our understanding of the principles deriving evolution of cellular organizations and their functions in a system level. In recent years, network alignment techniques have been applied to genome-scale PPI networks to predict evolutionary conserved modules. Although a wide variety of network alignment algorithms have been introduced, developing a scalable local network alignment algorithm with high accuracy is still challenging. Results We present a novel pairwise local network alignment algorithm, called LePrimAlign, to predict conserved modules between PPI networks of three different species. The proposed algorithm exploits the results of a pairwise global alignment algorithm with many-to-many node mapping. It also applies the concept of graph entropy to detect initial cluster pairs from two networks. Finally, the initial clusters are expanded to increase the local alignment score that is formulated by a combination of intra-network and inter-network scores. The performance comparison with state-of-the-art approaches demonstrates that the proposed algorithm outperforms in terms of accuracy of identified protein complexes and quality of alignments. Conclusion The proposed method produces local network alignment of higher accuracy in predicting conserved modules even with large biological networks at a reduced computational cost.

Observing the relaxation of molecular orientation in sheared liquid crystalline polymer solutions

1990 ◽  
Vol 48 (4) ◽  
pp. 1092-1093
Author(s):  
Wendy Putnam ◽  
Christopher Viney
Keyword(s):  
Molecular Orientation ◽  
Liquid Crystalline Polymer ◽  
Liquid Crystalline ◽  
Crystalline Polymer ◽  
Polymer Processing ◽  
Molecular Alignment ◽  
Global Alignment ◽  
Shear Direction ◽  
Axial Strength ◽  
Strength And Stiffness

Liquid crystalline polymers (solutions or melts) can be spun into fibers and films that have a higher axial strength and stiffness than conventionally processed polymers. These superior properties are due to the spontaneous molecular extension and alignment that is characteristic of liquid crystalline phases. Much of the effort in processing conventional polymers goes into extending and aligning the chains, while, in liquid crystalline polymer processing, the primary microstructural rearrangement involves converting local molecular alignment into global molecular alignment. Unfortunately, the global alignment introduced by processing relaxes quickly upon cessation of shear, and the molecular orientation develops a periodic misalignment relative to the shear direction. The axial strength and stiffness are reduced by this relaxation.Clearly there is a need to solidify the liquid crystalline state (i.e. remove heat or solvent) before significant relaxation occurs. Several researchers have observed this relaxation, mainly in solutions of hydroxypropyl cellulose (HPC) because they are lyotropic under ambient conditions.

Explore the mechanism of Swertia mussotii Franch. for hepatoprotective effects with iTRAQ-LC-MS/MS

2020 ◽  
Vol 23 ◽  
Author(s):  
Haixia Yun ◽  
Xinyu Wu ◽  
Yiwei Ding ◽  
Wendou Xiong ◽  
Xianglan Duan ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Carbon Tetrachloride ◽  
Liver Injury ◽  
Aspartate Aminotransferase ◽  
Alanine Aminotransferase ◽  
Total Bilirubin ◽  
Acute Liver Injury ◽  
Proteome Analysis ◽  
Ppi Networks ◽  
Hepatoprotective Effects

Background and Objective : A Tibetan traditional herb named Swertia mussotii Franch., also called “Zangyinchen” by the local people of Qinghai-Tibet area, has been used to protect the liver from injury for many years. However, the curative effect and molecular mechanism of the herb have not been demonstrated clearly. Materials and Methods: In our study, serum alanine aminotransferase, aspartate aminotransferase, total bilirubin levels were examined after S. mussotii Franch. treatment in the acute liver injury of the carbon tetrachloride-induced rat model. Then, Proteome Analysis was applied to explore the potential mechanism of SMT for hepatoprotective effects after iTRAQLC-MS/MS analysis (isobaric tag for relative and absolute quantification-liquid chromatograph-mass spectrometer with tandem mass spectrometry). Results: Serum results showed, alanine aminotransferase, aspartate aminotransferase, total bilirubin levels of rats with acute liver injury were all improved with SMT treatment. Moreover, Proteome Analysis suggested that, with S. Mussotii Franch. treatment, the levels of lipid catabolic process and lipid homeostasis were all enhanced. And the results of protein-protein interaction (PPI) analysis illustrated that these proteins assembled in PPI networks were found almost significantly enriched in response to lipid, negative regulation of lipase activity, response to lipopolysaccharide etc. Furthermore, the downregulated MRP14 and MRP8 proteins were found involved in the lipid metabolism, which may indicate the mechanism of SMT protection liver from ALI induced by carbon tetrachloride. Conclusion: SMT herb could play a role in hepatoprotection and alleviate the effect of acute liver injury by impacting the lipid metabolism associated biological process.

Axin PPI Networks: New Interacting Proteins and New Targets?

2016 ◽  
Vol 16 (30) ◽  
pp. 3678-3690
Author(s):  
Xiaomin Song ◽  
Wenwen Cai ◽  
Lin Li
Keyword(s):  
Interacting Proteins ◽  
New Targets ◽  
Ppi Networks

Identification of key mRNAs and lncRNAs involved in the effects of anti-TWEAK on Osteosarcoma

2020 ◽  
Vol 15 ◽  
Author(s):  
Mingxuan Yang ◽  
Liangtao Zhao ◽  
Xuchang Hu ◽  
Haijun Feng ◽  
Xuewen Kang
Keyword(s):  
Dna Replication ◽  
Signaling Pathway ◽  
Bioinformatics Analysis ◽  
Mapk Signaling ◽  
Migration And Invasion ◽  
Type I ◽  
Interferon Signaling ◽  
Nf Kappa B ◽  
Ppi Networks ◽  
Coexpression Networks

Background: Osteosarcoma (OS) is one of the most common primary malignant bone tumors in teenagers. Emerging studies demonstrated TWEAK and Fn14 were involved in regulating cancer cell differentiation, proliferation, apoptosis, migration and invasion. Objective: The present study identified differently expressed mRNAs and lncRNAs after anti-TWEAK treatment in OS cells using GSE41828. Methods: We identified 922 up-regulated mRNAs, 863 downregulated mRNAs, 29 up-regulated lncRNAs, and 58 down-regulated lncRNAs after anti-TWEAK treatment in OS cells. By constructing PPI networks, we identified several key proteins involved in anti-TWEAK treatment in OS cells, including MYC, IL6, CD44, ITGAM, STAT1, CCL5, FN1, PTEN, SPP1, TOP2A, and NCAM1. By constructing lncRNAs coexpression networks, we identified several key lncRNAs, including LINC00623, LINC00944, PSMB8-AS1, LOC101929787. Result: Bioinformatics analysis revealed DEGs after anti-TWEAK treatment in OS were involved in regulating type I interferon signaling pathway, immune response related pathways, telomere organization, chromatin silencing at rDNA, and DNA replication. Bioinformatics analysis revealed differently expressed lncRNAs after antiTWEAK treatment in OS were related to telomere organization, protein heterotetramerization, DNA replication, response to hypoxia, TNF signaling pathway, PI3K-Akt signaling pathway, Focal adhesion, Apoptosis, NF-kappa B signaling pathway, MAPK signaling pathway, FoxO signaling pathway. Conclusion: : This study provided useful information for understanding the mechanisms of TWEAK underlying OS progression and identifying novel therapeutic markers for OS.

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