Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 10 of 10 for “"Cytoscape"”.
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Refinement of Subnetwork Discovery Algorithm for Biological Networks
… information. JAM (jActiveModules) is a Cytoscape plugin developed to nd connected sets of genes with high levels of di erential expression. This network approach helps biologists to generate new hypotheses concerning the biological mechanisms underlying observed changes in gene …
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Architecture and Evolution of Xylem-related Gene Coexpression Networks in Poplars
… bioinformatics tools such as Gene Ontology and Cytoscape. In order to booster the accuracy of the findings, we have combined it with an evolutionary approach, synonymous and non-synonymous ratio (dN/dS) of the proteins to show the selective patterns of the genes in a comparative fashion between …
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Transcriptome Analysis of Sea Lamprey Embryogenesis
… previous adjacent stages, were analyzed using Cytoscape, an open source network program to further verify their functional roles. Genes TGFBR1 (protein kinase), SMAD2 (signal transducer), TRAF6 (signal transducer), PCNA (DNA replication), SLX4 (endonuclease), and PXN (focal adhesion) were …
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Knowledge-fused Identification of Condition-specific Rewiring of Dependencies in Biological Networks
… We developed an accompanying R package and Cytoscape plugin to provide both batch processing ability and user-friendly graphic interfaces. With the comprehensive software tools, we apply our method to several practically important biological problems to study how yeast response to stress, to …
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Functional discovery in the oxidative D-galacturonate assimilation pathway and development of the enzyme similarity web tool
… and easily. The networks can be viewed in Cytoscape and contain an aggregate of annotation data pulled from different sources (e.g., UniProt, GenomesOnline). The first part of this work (Chapter 2) describes the web tool and provides an example in which members of the enolase superfamily …
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Dimensionality Reduction, Feature Selection and Visualization of Biological Data
… we displayed the network view using Cytoscape; functional annotations using IPA and DAVID functional analysis tools; expression pattern using heat-map and parallel coordinates plot; and MD associated pathways using KEGG pathway diagrams. We also performed weighted MD pathway analysis, …
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Understanding grapevine responses to abscisic acid
… pathways affected by ABA were analyzed using the Cytoscape program with the BiNGO plug-in software. The results indicated that these genes were involved in several biological processes such as response to reactive oxygen species, response to light, and response to temperature stimulus. Protein …
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Clustering biological data by unraveling hidden transitive substructures
… as plugin for the standard network analysis tool Cytoscape. It provides results of similar or superior accuracy to those of alternative approaches. It is unique in that it features an easy-to-use clustering environment that contributes to all the important steps in a cluster analysis: (1) the …
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Sickle cell trait and targeted genomic variants in chronic kidney disease an African cohort
… pathway test using the Linux programme Cytoscape. Results The mean age of cases was 53 years (range 46-55 years), with 43% that were female; there were no age and sex significant differences with controls. We identified, an expected, association between CKD and various co-morbidities, …
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Pharmacological targets for treatment of retinal neurodegenerations: new perspectives [Nuove prospettive sui target farmacologici per il trattamento della neurodegenerazione retinica]
… vs. glaucoma). Mediante i software STRING e Cytoscape sono state messe in evidenza le reti di connessione tra i geni principalmente coinvolti nei campioni biologici analizzati, e attraverso un’analisi di centralità di queste reti sono stati evidenziati potenziali target farmacologici per il …