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Showing 1 to 20 of 67 for “"KEGG"”.
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Extending the Graphical Representation of four KEGG Pathways for a Better Understanding of Prostate Cancer Using Machine Learning of Graphical models
… It shows how the graphical representation of KEGG pathways can be refined using machine learning of graphical models. The focus mainly is on a set of graphical models called Bayesian networks. Throughout this thesis , different ways of learning Bayesian networks are discussed. The work is …
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PathMeld: A Methodology for The Unification of Metabolic Pathway Databases
… are the Kyoto Encyclopedia of Genes and Genomes (KEGG) and MetaCyc. The proliferation of biological databases in general raises several questions for the life scientist. Which of these databases is most accurate, most current, or most comprehensive? Do they have a standard format? Do they …
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Teak: A Novel Computational And Gui Software Pipeline For Reconstructing Biological Networks, Detecting Activated Biological Subnetworks, And Querying Biological Networks.
… biological networks from gene sets using the KEGG pathways as prior knowledge. The second and third modules query against the KEGG pathways using molecular profiling data and query graphs, respectively. In particular, the second module, also called TEAK, is a network partitioning module that …
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Network to pology In Human Protein Interaction Data Predicts Functional Association
… and the Kyoto Encyclopedia of Genes and Genomes (KEGG) as independent and unbiased benchmarks to evaluate our algorithms and methods within the human PPI network. We showed that, compared with the previous work from Samanta and Liang, our algorithm and methods developed in this study improved the …
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Cytoskeletal Gene Expression in Dental Pulp Stem Cells Under Inflammation-Induced Hypoxia
… pathway identification was facilitated through KEGG pathway analysis. Results: Our analysis revealed 1 over-expressed and 4 under-expressed genes that differed in normoxic from hypoxic conditions. The genes and pathways were identified in KEGG pathways overlaying expression values. Conclusion: …
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A robust pathfinding algorithm using chemical composition
… requires someone to complete manual curation. KEGG RPAIR database is an annotation to describe reactions in terms of reactant pairs and has been used for metabolic pathfinding. Here, I first study a few different centrality measures to identify currency metabolites and identify one better than …
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Longitudinal gene networks, canonical pathways and functional analysis of microarray data from Longissimus thoracis et lumborum muscle samples of early-weaned Angus steers
… of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and functional analysis was performed by the Database for Annotation, Visualization and Integrated Discovery (DAVID) bioinformatics software’s. ANOVA using a false discovery rate < 0.01 revealed ca. 4,300 differentially expressed genes (DEG) …
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Analisi dei profili di espressione dei microRNA: identificazione di biomarker nel suicidio
… and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to clarify the possible role of the identified miRNAs in biological mechanisms involved in suicide. Results from GO analysis indicated that miR-4286 and miR-186-5p regulate the expression of key genes involved in neuronal …
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SEA: a novel computational and GUI software pipeline for detecting activated biological sub-pathways
… have grown increasingly robust with the KEGG database at the forefront. Previous tools have color-coded the genes on different pathways using differential expression analysis. Unfortunately, they do not adequately capture the relationships of the genes amongst one another. Structure …
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Hybridising Organic Chemical and Synthetic Biological Reaction Data for Molecular Synthesis
… the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to create a hybrid dataset. The combined dataset was used to assemble synthetic pathways from multiple building blocks to a target molecule. Route assembly was performed using reinforcement learning, which was adapted to learn the …
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Nutritional modulation of the transcriptome in adipose, liver, and polymorphonuclear leukocytes in peripartal dairy cows
… via microarray technology. Subsequently, KEGG pathway analysis of 1806 differentially expressed genes (DEG; FDR < 0.05) was conducted using the Dynamic Impact Approach (DIA). The top 20 impacted (i.e.: most relevant) pathways fell into three KEGG categories: Metabolism, Genetic Information …
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Refinement of Subnetwork Discovery Algorithm for Biological Networks
… (Dendritic Cell) maturation microarray data and KEGG pathways to study the underlying mechanisms behind the DC maturation process, an essential part of the development of protective immunity to a number of infectious pathogens.
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Advancing Toxicology-Based Cancer Risk Assessment with Informatics
… in combination with well developed ontologies (Kegg/GO), which were at or below measured tumorigenic and precursor events. In conclusion, informatics was effective in advancing toxicology-based cancer risk assessment using databases and predictive techniques which fill critical gaps in its …
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Investigating the effect of paralogs on microarray gene-set analysis
… from databases such as the Gene Ontology (GO) or KEGG to group genes into sets based on their annotations. They aim to rank these gene sets in a way that reflects their relative importance in the experimental situation in question. The objective is that this approach reveals sets of genes with …
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A Tail-Based Test For Differential Expression Analysis and Pathway Analysis In Rna-Sequencing Data
… on non-small cell lung cancer pathways from KEGG pathway Database also demonstrates the proposed test is a powerful method in detecting differentially expressed pathways.</p>
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Transkriptomweite Untersuchungen von Prostata-Krebszelllinien im Kontext medizinischer Strahlentherapie
… eines Netzwerk-Scores konnten aus den GO- und KEGG-Datenbanken interessante Kategorien und Netzwerke abgeleitet werden, wobei insbesondere die GO-Kategorien Aldehyd-Dehydrogenase [NAD(P)+] Aktivität (GO:0004030) und der KEGG-Stoffwechselweg der O-Glykan Biosynthese (hsa00512) als relevante …
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Identifying Diagnostic Biomarkers: Gene Expression Profiling Leptin in Dental Pulp Tissue
… gene. The genes and pathways were identified in KEGG pathways overlaying expression values. Over-expressed (p<0.05) genes include ACSL1, LEP, LEPR and PRKAA2 and under-expressed (p<0.05) genes include MAPK8, NFKBIE, RELA. DPSCs in hypoxic conditions shows down-regulation of AMPK signaling, which …
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VANESA - A bioinformatics software application for the modeling, visualization, analysis, and simulation of biological networks in systems biology applications
… systems with information from the databases KEGG, MINT, IntAct, HPRD, and BRENDA. Additionally, experimental results can be expanded with database information to better analyze the investigated elements and processes in an overall context. This results in biological models, which enable …
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The role of prostate cancer microvesicles in epithelial mesenchymal transition
… Pathway analysis tools such as DAVID, PANTHER, KEGG and STRING were used to analyse the protein data. Importantly this study identified key proteins in PC3 MVs that may have contributed to the process of EMT, such as integrins which play a vital role in the biology of invasive carcinoma and …
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IMPLEMENTAZIONE DI DUE METODI PATHWAY TOPOLOGY-BASED PER L’ANALISI DELLA PERTURBAZIONE DI PATHWAY BIOLOGICI
… grazie anche all’integrazione dei pathway di KEGG con informazioni relative a interazioni microRNA-target e induzione dell’espressione di specifici microRNA da parte di specifici fattori della trascrizione.
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