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Full-Text Articles in Computational Biology
Extensions To Gene Set Enrichment, Zhen Jiang, Robert Gentleman
Extensions To Gene Set Enrichment, Zhen Jiang, Robert Gentleman
Bioconductor Project Working Papers
Motivation: Gene Set Enrichment Analysis (GSEA) has been developed recently to capture moderate but coordinated changes in the expression of sets of functionally related genes. We propose number of extensions to GSEA, which uses different statistics to describe the association between genes and phenotype of interest. We make use of dimension reduction procedures, such as principle component analysis to identify gene sets containing coordinated genes. We also address the problem of overlapping among gene sets in this paper.
Results: We applied our methods to the data come from a clinical trial in acute lymphoblastic leukemia (ALL) [1]. We identified interesting …
Visualizing Genomic Data, Robert Gentleman, Florian Hahne, Wolfgang Huber
Visualizing Genomic Data, Robert Gentleman, Florian Hahne, Wolfgang Huber
Bioconductor Project Working Papers
The advent of experimental techniques capable of probing biomolecules and cells at high levels of resolution has led to a rapid change in the methods used for the analysis of experimental molecular biology data. In this article we give an overview over visualization techniques and methods that can be used to assess various aspects of genomic data.