Identifying biological themes within lists of genes with EASE
Genome biologyPublished 25 April 2003Open access
Douglas A Hosack, Glynn Dennis, Brad T. Sherman, H. Clifford Lane, Richard A. Lempicki
Citations269
SJR quartileQ1
SJR score5.71
SNIP2.21
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
Abstract
EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE, and other high-throughput genomic data. The biological themes returned by EASE recapitulate manually determined themes in previously published gene lists and are robust to varying methods of normalization, intensity calculation and statistical selection of genes. EASE is a powerful tool for rapidly converting the results of functional genomics studies from "genes to themes."
Keywords
Biochemistry, Genetics and Molecular Biology
Proceedings of the National Academy of SciencesSignificance analysis of microarrays applied to the ionizing radiation response
10,671 Citations2001Virginia Goss Tusher, Robert Tibshirani +1 more
Proceedings of the National Academy of SciencesModel-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
3,182 Citations2000Cheng Li, Wing Hung Wong
A statistical model is proposed for the probe-level data, and model-based estimates for gene expression indexes are developed, which help to identify and handle cross-hybridizing probes and contaminating array regions.
Nature GeneticsMicroarray data normalization and transformation
2,007 Citations2002John Quackenbush
This review focuses on the much more mundane but indispensable tasks of 'normalizing' data from individual hybridizations to make meaningful comparisons of expression levels, and of 'transforming' them to select genes for further analysis and data mining.
Annual Review of Biomedical EngineeringDNA Microarray Technology: Devices, Systems, and Applications
1,063 Citations2002Michael J. Heller
This review covers applications of microarray devices and systems for pharmacogenomic research and drug discovery, infectious and genetic disease and cancer diagnostics, and forensic and genetic identification purposes.
Nature GeneticsFrom patterns to pathways: gene expression data analysis comes of age
581 Citations2002Donna K. Slonim
Proceedings of the National Academy of SciencesInfluences of aging and caloric restriction on the transcriptional profile of skeletal muscle from rhesus monkeys
387 Citations2001Tsuyoshi Kayo, David B. Allison +2 more
The results indicate that the induction of an oxidative stress-induced transcriptional response may be a common feature of aging in skeletal muscle of rodents and primates, but the extent to which CR modifies these responses may be species-specific.
Proceedings of the National Academy of SciencesGene expression and viral prodution in latently infected, resting CD4 <sup>+</sup> T cells in viremic versus aviremic HIV-infected individuals
176 Citations2003Tae‐Wook Chun, J. Shawn Justement +11 more
It is suggested that active viral replication has a significant impact on the physiologic state of resting CD4+ T cells in infected viremic patients and, in turn, allows release of HIV-1 without exogenous activation stimuli.
Proceedings of the National Academy of SciencesHIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication
164 Citations2002Claudia Cicala, James Arthos +12 more
Examination of transcriptional changes induced by gp120 in freshly isolated peripheral blood mononuclear cells and monocyte-derived-macrophages reveals a broad and complex transcriptional program conducive to productive infection with HIV.
Information SciencesOligonucleotide microarray data distribution and normalization
28 Citations2002I. A. Sidorov, Douglas A Hosack +5 more
It is shown that Affymetrix oligonucleotide probe signal distributions can be fitted by using a superposition of two normal or two extreme distributions, and that by using such distributions the authors can normalize data with high accuracy (parametric algorithm) and a second algorithm based on ranking of signal intensities which gave equal or better normalization than the parametric one.