GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
Eran Eden,Roy Navon,Roy Navon,Israel Steinfeld,Israel Steinfeld,Doron Lipson,Zohar Yakhini,Zohar Yakhini +7 more
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TLDR
GOrilla is a web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets, and its unique features and advantages over other threshold free enrichment tools include rigorous statistics, fast running time and an effective graphical representation.Abstract:
Since the inception of the GO annotation project, a variety of tools have been developed that support exploring and searching the GO database In particular, a variety of tools that perform GO enrichment analysis are currently available Most of these tools require as input a target set of genes and a background set and seek enrichment in the target set compared to the background set A few tools also exist that support analyzing ranked lists The latter typically rely on simulations or on union-bound correction for assigning statistical significance to the results GOrilla is a web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets This is particularly useful in many typical cases where genomic data may be naturally represented as a ranked list of genes (eg by level of expression or of differential expression) GOrilla employs a flexible threshold statistical approach to discover GO terms that are significantly enriched at the top of a ranked gene list Building on a complete theoretical characterization of the underlying distribution, called mHG, GOrilla computes an exact p-value for the observed enrichment, taking threshold multiple testing into account without the need for simulations This enables rigorous statistical analysis of thousand of genes and thousands of GO terms in order of seconds The output of the enrichment analysis is visualized as a hierarchical structure, providing a clear view of the relations between enriched GO terms GOrilla is an efficient GO analysis tool with unique features that make a useful addition to the existing repertoire of GO enrichment tools GOrilla's unique features and advantages over other threshold free enrichment tools include rigorous statistics, fast running time and an effective graphical representation GOrilla is publicly available at: http://cbl-gorillacstechnionacilread more
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In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta.
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References
More filters
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal ArticleDOI
Gene expression profiling predicts clinical outcome of breast cancer
Laura J. van't Veer,Hongyue Dai,Marc J. van de Vijver,Yudong D. He,Augustinus A. M. Hart,Mao Mao,Hans Peterse,Karin van der Kooy,Matthew J. Marton,Anke T. Witteveen,George J. Schreiber,Ron M. Kerkhoven,Christopher J. Roberts,Peter S. Linsley,René Bernards,Stephen H. Friend +15 more
TL;DR: DNA microarray analysis on primary breast tumours of 117 young patients is used and supervised classification is applied to identify a gene expression signature strongly predictive of a short interval to distant metastases (‘poor prognosis’ signature) in patients without tumour cells in local lymph nodes at diagnosis, providing a strategy to select patients who would benefit from adjuvant therapy.
Journal ArticleDOI
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Glynn Dennis,Brad T. Sherman,Douglas A. Hosack,Jun Jun Yang,Wei Gao,H. Clifford Lane,Richard A. Lempicki +6 more
TL;DR: DAMID is a web-accessible program that integrates functional genomic annotations with intuitive graphical summaries that assists in the interpretation of genome-scale datasets by facilitating the transition from data collection to biological meaning.
Journal ArticleDOI
BiNGO : a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
TL;DR: The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine whichGene Ontology terms are significantly overrepresented in a set of genes.
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