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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miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors
Espen Enerly,Israel Steinfeld,Kristine Kleivi,Kristine Kleivi,Suvi-Katri Leivonen,Miriam Ragle Aure,Hege G. Russnes,Jo Anders Rønneberg,Jo Anders Rønneberg,Hilde Johnsen,Roy Navon,Einar Andreas Rødland,Rami Mäkelä,Bjørn Naume,Merja Perälä,Olli Kallioniemi,Olli Kallioniemi,Vessela N. Kristensen,Vessela N. Kristensen,Zohar Yakhini,Zohar Yakhini,Anne Lise Børresen-Dale,Anne Lise Børresen-Dale +22 more
TL;DR: This study presents and analyzes data derived from expression profiling of 799 miRNAs in 101 primary human breast tumors, along with genome-wide mRNA profiles and extensive clinical information, to identify statistical significant differential expression of mi RNAs between molecular intrinsic subtypes, and between samples with different levels of proliferation.
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