gene set enrichment analysis
Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis
... Abstract Gene Set Enrichment Analysis (GSEA) is a basic tool for genomic data ...different gene sets results in shorter computing ...
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BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses
... on gene-by-gene statistical evaluation of differential expression can often miss this type of informative coordinated regulation of relevant sets of genes, because the fraction of genes individually ...
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Analysis of Genetically Regulated Gene Expression Identifies a Prefrontal PTSD Gene, SNRNP35, Specific to Military Cohorts
... all gene set analyses, we included only gene sets with at least ten genes and used the ‘‘competitive’’ P-value from ...our analysis includes largely EA individuals, we do not expect the ...
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Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants
... descriptive analysis of the gene ontologies associated with those ...Singular Enrichment Analysis (SEA) [59] in the absence of the traditional gene expression in- formation (thus no ...
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A Comparative Analysis of Perturbations Caused by a Gene Knock-out, a Dominant Negative Allele, and a Set of Peptide Aptamers
... a gene to a regulation by Fur determined its belonging to the different ...box enrichment rates within the population of the 196 retained genes (see “Experimental Procedures” and Supplemental ...each ...
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Semi-supervised consensus clustering for gene expression data analysis
... In reality, obtaining large amount of prior knowledge for gene expression datasets is difficult. Designing algorithms which work best with a small amount of prior knowledge, such as less than 20 pairwise ...
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Interpreting microarray experiments via co-expressed gene groups analysis
... exploit Gene Ontology (GO) we have generated: SGOD ...yeast gene using Saccharomyces Genome Database (SGD) 3 ...each gene and his parents preserving the hierarchical structure of ...whole set ...
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Dynamic Enrichment of Social Users' Interests
... The Enrichment Approach In this section, we detail our approach for enriching users ...needs. Enrichment in this context is done by analysing the environment of the user to detect relevant interests ...
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Data mining techniques for large-scale gene expression analysis
... The ranked data is often useful when mining the database for phenotypic trends across large sets of samples [47] (e.g., clustering sam- ples related to particular tumo[r] ...
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Towards the French Biomedical Ontology Enrichment
... As we have seen, this chapter introduced the state-of-the-art of terminology extrac- tion tasks. This chapter has highlighted the most relevant studies regarding this task. The most well-known approaches are based on ...
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CregNET: Meta-Analysis of Chlamydomonas reinhardtii Gene Regulatory Network
... yeast gene expres- sion profiling data, was ...in gene expres- sion series with no less than 8 ...from Gene Expression Omnibus (GEO) (Ron Edgar, Domrachev, and Lash, 2002 ...For gene ...
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Average case analysis of greedy algorithms for optimisation problems on set systems
... vertex set is E, each vertex of V being a hyperedge containing its incident ...dominating set, minimum vertex covering, maximum independent set, ...
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On name generation and set-based analysis in Dolev-Yao model
... Unité de recherche INRIA Sophia Antipolis 2004, route des Lucioles - BP 93 - 06902 Sophia Antipolis Cedex France Unité de recherche INRIA Lorraine : LORIA, Technopôle de Nancy-Brabois - [r] ...
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A Detailed Analysis of the KDD CUP 99 Data Set
... data set rather than analysis of the data, Mahoney and Chan [13] analyzed DARPA background network traffic and found evidence of simulation artifacts that could result in an overestimation of the performance ...
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Analysis and Mapping of an Updated Terrestrial Heat Flow Data Set
... Black lines correspond to the trends proposed by (Vitorello et al., 1980): (I) is surface heat flow, (II) is the reduced heat flow (surface heat flow minus upper crust radiogenic contrib[r] ...
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Analysis of the penA gene of Pseudomonas cepacia 249.
... With Streptomyces cacaoi, nucleotide sequence analy- sis of the r-lactamase coding region revealed several open reading frames which contain sequences typical of DNA- binding activator p[r] ...
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The paradox of enrichment in metaecosystems
... to enrichment (Jansen 1995, 2001; Hauzy et ...the enrichment in inorganic form to stabilize the metaecosystem, without increasing the consumer density in the sink such that the spatial flow direction would ...
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Dynamic Enrichment of Social Users' Interests
... lead to collaborative tagging systems [11]. The collaborative tagging behaviour, leads to creating a folksonomy introduced by [25]. Unlike the ontology, this folksonomy is not structured. Also, a tag may be a way to find ...
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Evaluation and Optimization of Clustering in Gene Expression Data Analysis
... given gene expression data ...data set to determine the cluster quality (the original information is kept ...data set, in the re-sampling validation method (Dudoit and Fridlyand 2002, Ben-Hur et ...
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Faustovirus E12 Transcriptome Analysis Reveals Complex Splicing in Capsid Gene
... Assistance Publique – Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (ME8I), Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Institut de Recherche pour le Développement IRD ...
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