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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Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease.
Magnus Tobiasson,Hani Abdulkadir,Andreas Lennartsson,Shintaro Katayama,Francesco Marabita,Ayla De Paepe,Mohsen Karimi,Kaarel Krjutškov,Kaarel Krjutškov,Elisabet Einarsdottir,Elisabet Einarsdottir,Michael Grövdal,Monika Jansson,Asmaa Ben Azenkoud,Lina Corddedu,Sören Lehmann,Sören Lehmann,Karl Ekwall,Juha Kere,Juha Kere,Eva Hellström-Lindberg,Johanna Ungerstedt +21 more
TL;DR: It is concluded that the marked induction of gene expression only partly could be explained by epigenetic changes, and proposed that activation of ERVs may contribute to the clinical effects of Aza in MDS.
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Revisiting demographic processes in cattle with genome-wide population genetic analysis.
Pablo Orozco-terWengel,Mario Barbato,Ezequiel L. Nicolazzi,Filippo Biscarini,Marco Milanesi,Wyn Davies,Don Williams,Alessandra Stella,Paolo Ajmone-Marsan,Michael William Bruford +9 more
TL;DR: The results suggest modern cross-breeding and ancient hybridisation events have both played an important role, including with animals of indicine origin, and additional demographic complexity of modern European cattle is uncovered.
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Bosutinib, dasatinib, imatinib, nilotinib, and ponatinib differentially affect the vascular molecular pathways and functionality of human endothelial cells.
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Comparative analysis reveals a role for TGF-β in shaping the residency-related transcriptional signature in tissue-resident memory CD8+ T cells
Artika P. Nath,Artika P. Nath,Artika P. Nath,Asolina Braun,Asolina Braun,Scott C. Ritchie,Scott C. Ritchie,Francis R. Carbone,Laura K. Mackay,Thomas Gebhardt,Michael Inouye +10 more
TL;DR: Findings show that TGF-β has a broad footprint in establishing the residency-specific transcriptional profile of TRM cells, which is detectable inTRM cells from diverse tissues, and suggest that constitutive T GF-β signaling might be involved for their long-term persistence at tissue sites.
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