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» Extensions to gene set enrichment
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BMCBI
2008
173views more  BMCBI 2008»
13 years 10 months ago
Gene Vector Analysis (Geneva): A unified method to detect differentially-regulated gene sets and similar microarray experiments
Background: Microarray experiments measure changes in the expression of thousands of genes. The resulting lists of genes with changes in expression are then searched for biologica...
Stephen W. Tanner, Pankaj Agarwal
BMCBI
2010
154views more  BMCBI 2010»
13 years 10 months ago
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data
Background: A major goal of molecular biology is determining the mechanisms that control the transcription of genes. Motif Enrichment Analysis (MEA) seeks to determine which DNA-b...
Robert C. McLeay, Timothy L. Bailey
BMCBI
2010
160views more  BMCBI 2010»
13 years 10 months ago
Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data
Background: Use of alternative gene promoters that drive widespread cell-type, tissue-type or developmental gene regulation in mammalian genomes is a common phenomenon. Chromatin ...
Ravi Gupta, Priyankara Wikramasinghe, Anirban Bhat...
BMCBI
2005
140views more  BMCBI 2005»
13 years 9 months ago
Dissecting systems-wide data using mixture models: application to identify affected cellular processes
Background: Functional analysis of data from genome-scale experiments, such as microarrays, requires an extensive selection of differentially expressed genes. Under many condition...
J. Peter Svensson, Renée X. de Menezes, Ing...
BMCBI
2005
77views more  BMCBI 2005»
13 years 9 months ago
The Gene Set Builder: collation, curation, and distribution of sets of genes
Background: In bioinformatics and genomics, there are many applications designed to investigate the common properties for a set of genes. Often, these multi-gene analysis tools at...
Dimas Yusuf, Jonathan S. Lim, Wyeth W. Wasserman