PAEA
Computational Tool
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General Information
DescriptionEnrichment analysis tool implementing the principal angle method
Homepagehttp://amp.pharm.mssm.edu/PAEA/
Publications
Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool
Neil R. Clark; Maciej Szymkiewicz; Zichen Wang; Caroline D. Monteiro; Matthew R. Jones; Avi Ma’ayan
Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community.
Metrics:
Canned Analyses generated by the tool

Dataset Accession
Tool Name
Organism
Cell Type
Disease Name
Drug Name
Hs Gene Symbol
Pert Type
Mm Gene Symbol

Enrichment analysis of genes dysregulated in acute myocardial infarction
An enrichment analysis was performed on the top most dyresgulated genes determined by appl...
Enrichment analysis of genes dysregulated following Imatinib treatment
An enrichment analysis was performed on the top most dyresgulated genes determined by appl...
Enrichment analysis of genes dysregulated following Imatinib treatment
An enrichment analysis was performed on the top most dyresgulated genes determined by appl...
Enrichment analysis of genes dysregulated following Imatinib treatment
An enrichment analysis was performed on the top most dyresgulated genes determined by appl...
Enrichment analysis of genes dysregulated following Imatinib treatment
An enrichment analysis was performed on the top most dyresgulated genes determined by appl...
Enrichment analysis of genes dysregulated following Imatinib treatment
An enrichment analysis was performed on the top most dyresgulated genes determined by appl...
Enrichment analysis of genes dysregulated following Imatinib treatment
An enrichment analysis was performed on the top most dyresgulated genes determined by appl...
Enrichment analysis of genes dysregulated following Imatinib treatment
An enrichment analysis was performed on the top most dyresgulated genes determined by appl...
Enrichment analysis of genes dysregulated following Imatinib treatment
An enrichment analysis was performed on the top most dyresgulated genes determined by appl...
Enrichment analysis of genes dysregulated following Celecoxib treatment
An enrichment analysis was performed on the top most dyresgulated genes determined by appl...
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Datasets analyzed by the tool

Keyword
Tool Name

GSE50588
The Functional Consequences of Variation in Transcription Factor Binding
294
GSE6930
Cytosine arabinoside effect on Ewing's sarcoma cell line: time course and dose response
119
GSE7002
Formaldehyde effect on nasal epithelium: dose response and time course
119
GSE47856
Expression data from cultured human ovarian carcinoma cell lines with and without Cisplatin treatment
119
GSE35366
Models of Neuronal Migration Defects: time course
112
GSE490
Pharmacogenomic effect of corticosteroid in skeletal muscle
112
GSE47150
Embryonic primary cortical neuron response to knockdown of multiple autism candidate genes
112
GSE15129
Coenzyme Q10-dependent gene expression in SAMP1 mice tissues
105
GSE60413
Parkinson Phenotype in Aged PINK1-Deficient Mice Is Accompanied by Progressive Mitochondrial Dysfunction in Absence of Neurodegeneration
105
GSE18344
Nrf2-deficient lung response to cigarette smoke: dose response and time course
98
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