GeneTrail—advanced gene set enrichment analysis
Christina Backes,Andreas Keller,Jan Kuentzer,Benny Kneissl,Nicole Comtesse,Yasser A. Elnakady,Rolf Müller,Eckart Meese,Hans-Peter Lenhof +8 more
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TLDR
GeneTrail's statistics module includes a novel dynamic-programming algorithm that improves the P-value computation of GSEA methods considerably and is freely accessible at http://genetrail.uni-sb.de.Abstract:
We present a comprehensive and efficient gene set analysis tool, called 'GeneTrail' that offers a rich functionality and is easy to use. Our web-based application facilitates the statistical evaluation of high-throughput genomic or proteomic data sets with respect to enrichment of functional categories. GeneTrail covers a wide variety of biological categories and pathways, among others KEGG, TRANSPATH, TRANSFAC, and GO. Our web server provides two common statistical approaches, 'Over-Representation Analysis' (ORA) comparing a reference set of genes to a test set, and 'Gene Set Enrichment Analysis' (GSEA) scoring sorted lists of genes. Besides other newly developed features, GeneTrail's statistics module includes a novel dynamic-programming algorithm that improves the P-value computation of GSEA methods considerably. GeneTrail is freely accessible at http://genetrail.bioinf.uni-sb.de.read more
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Book ChapterDOI
Computational Challenges and -omics Approaches for the Identification of microRNAs and Targets
Ioannis S. Vlachos,Ioannis S. Vlachos,Georgios Georgakilas,Georgios Georgakilas,Spyros Tastsoglou,Spyros Tastsoglou,Maria D. Paraskevopoulou,Maria D. Paraskevopoulou,Dimitra Karagkouni,Dimitra Karagkouni,Artemis G. Hatzigeorgiou,Artemis G. Hatzigeorgiou +11 more
TL;DR: This chapter aims to provide an overview of the available state-of-the-art tools, web servers, and databases utilized in miRNA research, covering an extensive scope ranging from miRNA annotation, promoter identification, and transcription to the identification of miRNA-controlled pathways.
SURVEY AND SUMMARY Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
TL;DR: A comprehensive survey of bioinformatics enrichment tools can be found in this paper, where tools are uniquely categorized into three major classes, according to their underlying enrichment algorithms, and a more comprehensive and up-to-date view regarding the advantages, pitfalls and recent trends is provided.
Patent
Blood-based gene expression signatures in lung cancer
TL;DR: In this article, a method for diagnosing or detecting lung cancer in human subjects based on ribonucleic acid (RNA) expression, in particular based on RNA from blood, was presented.
Journal ArticleDOI
Expression of Cytokine-Coding Genes BMP8B, LEFTY1 and INSL5 Could Distinguish between Ulcerative Colitis and Crohn's Disease.
TL;DR: In this paper, an expression profile of cytokines in UC and CD, using bioinformatics approach, and experimental validation of expression of the selected genes, was provided, and the expression of genes LEFTY1 and BMP8B was statistically significant when comparing UC and Crohn's disease in colon.
Posted ContentDOI
Environmental perturbations lead to extensive directional shifts in RNA processing
Allison L. Richards,Donovan Watza,Anthony S Findley,Adnan Alazizi,Xiaoquan Wen,Athma A. Pai,Roger Pique-Regi,Francesca Luca +7 more
TL;DR: It is demonstrated that RNA processing is dramatically changed in response to environmental perturbations through specific mechanisms regulated by trans factors, and that the changes to first exon usage are likely dependent on changes in transcription factor binding.
References
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