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BMCBI
2011
11 years 14 days ago
Appearance frequency modulated gene set enrichment testing
Background: Gene set enrichment testing has helped bridge the gap from an individual gene to a systems biology interpretation of microarray data. Although gene sets are defined a ...
Jun Ma, Maureen A. Sartor, H. V. Jagadish
JCP
2008
92views more  JCP 2008»
11 years 5 months ago
A Hierarchical Gene-Set Genetic Algorithm
In this paper, gene sets, instead of individual genes, are used in the genetic process to speed up convergence. A gene-set mutation operator is proposed, which can make several nei...
Tzung-Pei Hong, Min-Thai Wu
JBI
2008
159views Bioinformatics» more  JBI 2008»
11 years 5 months ago
SEGS: Search for enriched gene sets in microarray data
Gene Ontology (GO) terms are often used to interpret the results of microarray experiments. The most common approach is to perform Fisher's exact tests to find gene sets anno...
Igor Trajkovski, Nada Lavrac, Jakub Tolar
BMCBI
2007
112views more  BMCBI 2007»
11 years 5 months ago
Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis
Background: Gene clustering has been widely used to group genes with similar expression pattern in microarray data analysis. Subsequent enrichment analysis using predefined gene s...
Tae-Min Kim, Yeun-Jun Chung, Mun-Gan Rhyu, Myeong ...
BMCBI
2008
88views more  BMCBI 2008»
11 years 5 months ago
Microarray-based gene set analysis: a comparison of current methods
Background: The analysis of gene sets has become a popular topic in recent times, with researchers attempting to improve the interpretability and reproducibility of their microarr...
Sarah Song, Michael A. Black
BMCBI
2008
173views more  BMCBI 2008»
11 years 5 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
2007
157views more  BMCBI 2007»
11 years 5 months ago
Improving gene set analysis of microarray data by SAM-GS
Background: Gene-set analysis evaluates the expression of biological pathways, or a priori defined gene sets, rather than that of individual genes, in association with a binary ph...
Irina Dinu, John D. Potter, Thomas Mueller, Qi Liu...
BMCBI
2010
123views more  BMCBI 2010»
11 years 5 months ago
Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context
Background: Different microarray studies have compiled gene lists for predicting outcomes of a range of treatments and diseases. These have produced gene lists that have little ov...
Gad Abraham, Adam Kowalczyk, Sherene Loi, Izhak Ha...
AUSAI
2007
Springer
11 years 9 months ago
Hybrid Methods to Select Informative Gene Sets in Microarray Data Classification
Abstract. One of the key applications of microarray studies is to select and classify gene expression profiles of cancer and normal subjects. In this study, two hybrid approaches
Pengyi Yang, Zili Zhang
AIME
2007
Springer
11 years 11 months ago
Interpreting Gene Expression Data by Searching for Enriched Gene Sets
This paper presents a novel method integrating gene-gene interaction information and Gene Ontology for the construction of new gene sets that are potentially enriched. Enrichment o...
Igor Trajkovski, Nada Lavrac
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