Identification of Essential Proteins in Yeast Using Mean Weighted Average and Recursive Feature Elimination

2019 ◽  
Vol 12 (1) ◽  
pp. 5-10 ◽  
Author(s):  
Sivagnanam Rajamanickam Mani Sekhar ◽  
Siddesh Gaddadevara Matt ◽  
Sunilkumar S. Manvi ◽  
Srinivasa Krishnarajanagar Gopalalyengar
Keyword(s):  
Drug Design ◽  
Weighted Average ◽  
Living Organism ◽  
Experimental Result ◽  
Recursive Feature Elimination ◽  
Protein Interaction Data ◽  
Essential Proteins ◽  
Protein Protein Interaction ◽  
Result Show ◽  
Better Than

Background: Essential proteins are significant for drug design, cell development, and for living organism survival. A different method has been developed to predict essential proteins by using topological feature, and biological features. Objective: Still it is a challenging task to predict essential proteins effectively and timely, as the availability of protein protein interaction data depends on network correctness. Methods: In the proposed solution, two approaches Mean Weighted Average and Recursive Feature Elimination is been used to predict essential proteins and compared to select the best one. In Mean Weighted Average consecutive slot data to be taken into aggregated count, to get the nearest value which considered as prescription for the best proteins for the slot, where as in Recursive Feature Elimination method whole data is spilt into different slots and essential protein for each slot is determined. Results: The result shows that the accuracy using Recursive Feature Elimination is at-least nine percentages superior when compared to Mean Weighted Average and Betweenness centrality. Conclusion: Essential proteins are made of genes which are essential for living being survival and drug design. Different approaches have been proposed to anticipate essential proteins using either experimental or computation methods. The experimental result show that the proposed work performs better than other approaches.

PREDICTION OF ESSENTIAL PROTEINS BASED ON EDGE CLUSTERING COEFFICIENT AND GENE ONTOLOGY INFORMATION

2014 ◽  
Vol 22 (03) ◽  
pp. 339-351 ◽  
Author(s):  
JIAWEI LUO ◽  
NAN ZHANG
Keyword(s):  
Gene Ontology ◽  
Network Topology ◽  
Clustering Coefficient ◽  
Ppi Network ◽  
Essential Proteins ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Survival And Development ◽  
Gene Ontology Information ◽  
Better Than

Essential proteins are important for the survival and development of organisms. Lots of centrality algorithms based on network topology have been proposed to detect essential proteins and achieve good results. However, most of them only focus on the network topology, but ignore the false positive (FP) interactions in protein–protein interaction (PPI) network. In this paper, gene ontology (GO) information is proposed to measure the reliability of the edges in PPI network and we propose a novel algorithm for identifying essential proteins, named EGC algorithm. EGC algorithm integrates topology character of PPI network and GO information. To validate the performance of EGC algorithm, we use EGC and other nine methods (DC, BC, CC, SC, EC, LAC, NC, PEC and CoEWC) to identify the essential proteins in the two different yeast PPI networks: DIP and MIPS. The results show that EGC is better than the other nine methods, which means adding GO information can help in predicting essential proteins.

scholarly journals Performance Analysis of Solar Tray Dryer for Cassava Starch

2018 ◽  
Vol 156 ◽  
pp. 05008 ◽  
Author(s):  
Suherman Suherman ◽  
Mohammad Djaeni ◽  
Dyah H. Wardhani ◽  
Mukhtar Dzaki R ◽  
Muhammad N. Bagas F
Keyword(s):  
Moisture Content ◽  
Solar Collector ◽  
Initial Moisture Content ◽  
Cassava Starch ◽  
Experimental Result ◽  
Drying Rate ◽  
Air Humidity ◽  
Solar Dryer ◽  
Result Show ◽  
Better Than

The main objective of this study is to analyze the performance of solar tray dryyer for cassava starch. The solar tray dryer is made of glass and iron shaped dryer and box, where the solar collector is made of black painted iron plate. The initial moisture content of cassava starch is 50% wet bases. The experimental result show the moisture content of starch decrease rapidly in 8 hours of drying the first day until 14% moisture content. Further drying able to dry starch to 8% water content. The water temperature in solar dryer can reach 60°C was higher than the ambient of 32°C. Furthermore, the air humidity relative in the solar dryer can drop dramatically to 30% is lower than the ambient 80%. Maximum drying rate can reach up to 0.2 g/h. Thermal efficiency of the dryer can reach 40%. The performance of this solar dryer is much better than the sun dryer which veing piloted in this study

scholarly journals Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Albert T. Young ◽  
Xavier Carette ◽  
Michaela Helmel ◽  
Hanno Steen ◽  
Robert N. Husson ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Mycobacterium Tuberculosis ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Protein Interaction Data ◽  
Kinase Inhibition ◽  
Protein Protein Interaction ◽  
Downstream Effects ◽  
Regulate Cell Growth ◽  
Regulatory Effects

AbstractThe ability of Mycobacterium tuberculosis (Mtb) to adapt to diverse stresses in its host environment is crucial for pathogenesis. Two essential Mtb serine/threonine protein kinases, PknA and PknB, regulate cell growth in response to environmental stimuli, but little is known about their downstream effects. By combining RNA-Seq data, following treatment with either an inhibitor of both PknA and PknB or an inactive control, with publicly available ChIP-Seq and protein–protein interaction data for transcription factors, we show that the Mtb transcription factor (TF) regulatory network propagates the effects of kinase inhibition and leads to widespread changes in regulatory programs involved in cell wall integrity, stress response, and energy production, among others. We also observe that changes in TF regulatory activity correlate with kinase-specific phosphorylation of those TFs. In addition to characterizing the downstream regulatory effects of PknA/PknB inhibition, this demonstrates the need for regulatory network approaches that can incorporate signal-driven transcription factor modifications.

scholarly journals Proteome Profiling of PMJ2-R and Primary Peritoneal Macrophages

2021 ◽  
Vol 22 (12) ◽  
pp. 6323
Author(s):  
Alexander L. Rusanov ◽  
Peter M. Kozhin ◽  
Olga V. Tikhonova ◽  
Victor G. Zgoda ◽  
Dmitry S. Loginov ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Living Organism ◽  
Peritoneal Macrophages ◽  
In Vitro Models ◽  
Individual Characteristics ◽  
Essential Proteins ◽  
Comparative Proteomic Analysis ◽  
Immortalized Cell ◽  
The Individual

In vitro models are often used for studying macrophage functions, including the process of phagocytosis. The application of primary macrophages has limitations associated with the individual characteristics of animals, which can lead to insufficient standardization and higher variability of the obtained results. Immortalized cell lines do not have these disadvantages, but their responses to various signals can differ from those of the living organism. In the present study, a comparative proteomic analysis of immortalized PMJ2-R cell line and primary peritoneal macrophages isolated from C57BL/6 mice was performed. A total of 4005 proteins were identified, of which 797 were quantified. Obtained results indicate significant differences in the abundances of many proteins, including essential proteins associated with the process of phagocytosis, such as Elmo1, Gsn, Hspa8, Itgb1, Ncf2, Rac2, Rack1, Sirpa, Sod1, C3, and Msr1. These findings indicate that outcomes of studies utilizing PMJ2-R cells as a model of peritoneal macrophages should be carefully validated. All MS data are deposited in ProteomeXchange with the identifier PXD022133.

scholarly journals Numerical Study of Pressure Attenuation Effect on Tunnel Structures Subjected to Blast Loads

2021 ◽  
Vol 11 (12) ◽  
pp. 5646
Author(s):  
Cheng-Wei Hung ◽  
Ying-Kuan Tsai ◽  
Tai-An Chen ◽  
Hsin-Hung Lai ◽  
Pin-Wen Wu
Keyword(s):  
Numerical Simulation ◽  
Orifice Plate ◽  
Experimental Result ◽  
Scale Model ◽  
Pressure Reduction ◽  
Expansion Chamber ◽  
Pressure Relief ◽  
Attenuation Effect ◽  
The One ◽  
Better Than

This study used experimental and numerical simulation methods to discuss the attenuation mechanism of a blast inside a tunnel for different forms of a tunnel pressure reduction module under the condition of a tunnel near-field explosion. In terms of the experiment, a small-scale model was used for the explosion experiments of a tunnel pressure reduction module (expansion chamber, one-pressure relief orifice plate, double-pressure relief orifice plate). In the numerical simulation, the pressure transfer effect was evaluated using the ALE fluid–solid coupling and mapping technique. The findings showed that the pressure attenuation model changed the tunnel section to diffuse, reduce, or detour the pressure transfer, indicating the blast attenuation effect. In terms of the effect of blast attenuation, the double-pressure relief orifice plate was better than the one-pressure relief orifice plate, and the single-pressure relief orifice plate was better than the expansion chamber. The expansion chamber attenuated the blast by 30%, the one-pressure relief orifice plate attenuated the blast by 51%, and the double-pressure relief orifice plate attenuated the blast by 82%. The blast attenuation trend of the numerical simulation result generally matched that of the experimental result. The results of this study can provide a reference for future protective designs and reinforce the U.S. Force regulations.

Sign in / Sign up

Export Citation Format

Share Document