Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods
暂无分享,去创建一个
[1] David B. Allison,et al. A mixture model approach for the analysis of microarray gene expression data , 2002 .
[2] Peter J. Park,et al. A multivariate approach for integrating genome-wide expression data and biological knowledge , 2006, Bioinform..
[3] Michael A. Black,et al. Microarray-based gene set analysis: a comparison of current methods , 2008, BMC Bioinformatics.
[4] Seon-Young Kim,et al. Gene-set approach for expression pattern analysis , 2008, Briefings Bioinform..
[5] R. Tibshirani,et al. On testing the significance of sets of genes , 2006, math/0610667.
[6] Korbinian Strimmer,et al. BMC Bioinformatics BioMed Central Methodology article A general modular framework for gene set enrichment analysis , 2009 .
[7] M. Daly,et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.
[8] Zhiping Weng,et al. Gene set enrichment analysis: performance evaluation and usage guidelines , 2012, Briefings Bioinform..
[9] M. Kendall. Statistical Methods for Research Workers , 1937, Nature.
[10] P.-C.-F. Daunou,et al. Mémoire sur les élections au scrutin , 1803 .
[11] Qi Zheng,et al. GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis , 2008, Nucleic Acids Res..
[12] Léon Personnaz,et al. Enrichment or depletion of a GO category within a class of genes: which test? , 2007, Bioinform..
[13] P. Park,et al. Discovering statistically significant pathways in expression profiling studies. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[14] J. Nielsen,et al. Uncovering transcriptional regulation of metabolism by using metabolic network topology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[15] Seon-Young Kim,et al. PAGE: Parametric Analysis of Gene Set Enrichment , 2005, BMC Bioinform..
[16] James J. Chen,et al. Multivariate analysis of variance test for gene set analysis , 2009, Bioinform..
[17] Jens Nielsen,et al. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks , 2008, BMC Systems Biology.
[18] M. McCarthy,et al. Interrogating Type 2 Diabetes Genome-Wide Association Data Using a Biological Pathway-Based Approach , 2009, Diabetes.
[19] Intawat Nookaew,et al. BioMet Toolbox: genome-wide analysis of metabolism , 2010, Nucleic Acids Res..
[20] Gordon K. Smyth,et al. limma: Linear Models for Microarray Data , 2005 .
[21] Martin Kuiper,et al. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks , 2005, Bioinform..
[22] U. Mansmann,et al. Testing Differential Gene Expression in Functional Groups , 2005, Methods of Information in Medicine.
[23] Jiankai Xu,et al. DBGSA: a novel method of distance-based gene set analysis , 2012, Journal of Human Genetics.
[24] E. Suchman,et al. The American Soldier: Adjustment During Army Life. , 1949 .
[25] Brad T. Sherman,et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery , 2003, Genome Biology.
[26] R. Tibshirani,et al. A tail strength measure for assessing the overall univariate significance in a dataset. , 2005, Biostatistics.
[27] Ralf Zimmer,et al. Rigorous assessment of gene set enrichment tests , 2012, Bioinform..
[28] Wenjun Cao,et al. Statistical and Biological Evaluation of Different Gene Set Analysis Methods , 2011 .
[29] Jelle J. Goeman,et al. A global test for groups of genes: testing association with a clinical outcome , 2004, Bioinform..
[30] T. Speed,et al. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. , 2004, Bioinformatics.
[31] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[32] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[33] B. Fridley,et al. Self-Contained Gene-Set Analysis of Expression Data: An Evaluation of Existing and Novel Methods , 2010, PloS one.
[34] Ulrich Mansmann,et al. GlobalANCOVA: exploration and assessment of gene group effects , 2008, Bioinform..
[35] Natapol Pornputtapong,et al. Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT , 2012, PLoS Comput. Biol..
[36] I. Nookaew,et al. A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae , 2012, Nucleic acids research.
[37] Rafael A. Irizarry,et al. Bioinformatics and Computational Biology Solutions using R and Bioconductor , 2005 .
[38] Peter Bühlmann,et al. Analyzing gene expression data in terms of gene sets: methodological issues , 2007, Bioinform..
[39] Gordon K Smyth,et al. Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .
[40] Brad T. Sherman,et al. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.