Pathway and gene set analysis
Efficient gene set analysis of high-throughput data : From omics to pathway architecture of health and disease
... at gene level data is analyzed (Section ...to gene-level genome-wide DNA methylation by several approaches, such as taking the average of the methy- lation levels of all CpGs mapping to the genomic region ...
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GAGE: generally applicable gene set enrichment for pathway analysis
... a gene sets to the whole set background, whereas PAGE uses a one-sample ...target gene set distribu- tion as well as the background distribution (Formula 1), while a one-sample z-test only ...
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Gene set analysis methods: a systematic comparison
... Based on these results, we can now form practical recommendations for end users. Overall, the most powerful method was sigPathway; however, GSEA with the user- calculated q-values has very similar performance and detects ...
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PAGE: Parametric Analysis of Gene Set Enrichment
... data analysis across various microarray platforms and biological ...for gene sets rather than individual ...level analysis meth- ods (Table 2) and different microarray platforms (Table 3), in each ...
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Weighted-SAMGSR: Combining Significance Analysis of Microarray-Gene Set Reduction Algorithm with Pathway Topology-Based Weights to Select Relevant Genes
... a pathway-based feature selection method that incorporates biological information within pathways during the process of feature selection usually outperforms a gene-based feature selection algorithm in ...
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Down-weighting overlapping genes improves gene set analysis
... new gene set analysis method that computes a gene set score as the mean of absolute values of weighted moderated gene ...The gene weights are designed to emphasize the ...
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Patient oriented gene set analysis for cancer mutation data
... one gene at the time, conventional gene set approaches are not able to differentiate between two very different ...a gene set including ten genes, and suppose ten different mutations ...
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GAGE: generally applicable gene set enrichment for pathway analysis
... full set of 17000 ...testing gene sets with con- trolled levels of differential expression (or degrees of enrichment in up- or down- regulated genes, details described in ...testing gene sets, and ...
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Network enrichment analysis: extension of gene-set enrichment analysis to gene networks
... First the mean and variance of FGS scores are given in Figure S2 of the Additional file 1 Report. The cancer- related pathways were neither the most enriched nor the most variable. Many other signaling KEGG pathways ...
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Finding pathway regulators: gene set approach using peak identification algorithms
... Heather J Cordell, Mariza de Andrade, Marie-Claude Babron, ...
Genetic Analysis Workshop 15: Gene Expression Analysis and Approaches to Detecting Multiple Functional Loci
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Gene Set Coregulated by the Saccharomyces cerevisiae Nonsense-Mediated mRNA Decay Pathway
... blot analysis of total RNA harvested from isogenic yeast strains AAY334 (UPF1, upper image) and AAY335 (upf1 ⌬ , lower image) at the indicated time points (in minutes) following arrest of ...
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Genomic analysis of metabolic pathway gene expression in mice
... regulate pathway genes were identified by analyzing for over-representation of identified pathway- associated gene eQTLs among eQTLs of the set of most differ- entially expressed genes in a ...
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CiteSeerX — Gene set enrichment in eQTL data identifies novel annotations and pathway regulators.
... our analysis on ‘‘trans-eQTL bands’’, defined as instances in which the expression patterns of many genes were all associated to a common genetic ...functional gene sets representing known biological ...
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GScluster: Network-weighted gene-set clustering analysis
... This pathway was the most highly connected (degree = 29) among the entire list of gene-sets in the pMM gene-set ...activation pathway is connected to many related cell signaling path- ...
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A Bayesian Approach to Pathway Analysis by Integrating Gene–Gene Functional Directions and Microarray Data
... microarray analysis to understand the gene expression patterns at distinct stages of osteoprogenitor ...observed gene expression changes based on a heterogenous cell mixture are associated with fully ...
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Multi-membership gene regulation in pathway based microarray analysis
... at Gene Expression omnibus (GEO) [25], platform GPL3503 [26], that contain a large number of expressed Urea Cycle ...Cycle pathway consists of 16 single-membership and 12 multi-member- ship ...each ...
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Multi-membership gene regulation in pathway based microarray analysis
... at Gene Expression omnibus (GEO) [25], platform GPL3503 [26], that contain a large number of expressed Urea Cycle ...Cycle pathway consists of 16 single-membership and 12 multi-member- ship ...each ...
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Weighted-SAMGSR: combining significance analysis of microarray-gene set reduction algorithm with pathway topology-based weights to select relevant genes
... major pathway databases. Therefore, the genes inside one specific pathway might be more likely to function together for the cancer cases, making the underlying assumption of the SAMGSR algorithm more ...
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Absolute Enrichment: Gene Set Enrichment Analysis for Homeostatic Systems
... ‘downregulated’. Gene sets are not necessarily pathways and GO gene categories should not be mixed At the GO website, it is stated that ‘A biological process is a recognized series of events or molecular ...
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Pathway and gene set activation measurement from mRNA expression data: the tissue distribution of human pathways
... our analysis, the PCA metric was the most sensitive at dis- criminating between two subgroups across multiple data sets and the least affected by incoherent gene ...the gene sets they were measuring ...
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