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
Citations
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Loss of Function of Arabidopsis C-Terminal Domain Phosphatase-Like1 Activates Iron Deficiency Responses at the Transcriptional Level
TL;DR: It is proposed that the cpl1 mutations enhance Fe deficiency signaling and promote cross talk with a branch of the osmotic stress/ABA signaling pathway.
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Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data
TL;DR: A new methodology that integrates microarray and TF binding data for unraveling transcriptional regulatory networks based on a two-stage constrained matrix decomposition model that identifies biologically more meaningful transcriptional modules relating to specific TFs.
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Genetic and transcriptional analysis of human host response to healthy gut microbiota.
Allison L. Richards,Michael B. Burns,Adnan Alazizi,Luis B. Barreiro,Roger Pique-Regi,Ran Blekhman,Francesca Luca +6 more
TL;DR: A novel experimental system is described to define the transcriptional response induced by the microbiota for human cells and to shed light on the molecular mechanisms underlying host-gut microbiota interactions that can be used to identify putative mechanisms for the interplay between host genetics and the microbiota in health and disease.
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Predicting Gene Ontology Function of Human MicroRNAs by Integrating Multiple Networks.
TL;DR: An integrated model, PmiRGO, is proposed to infer the gene ontology (GO) functions of mi RNAs by integrating multiple data sources, including the expression profiles of miRNAs, miRNA-target interactions, and protein-protein interactions (PPI).
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InCroMAP: Integrated analysis of Cross-platform MicroArray and Pathway data
TL;DR: The available features of InCroMAP range from visualization of DNA methylation data over annotation of microRNA targets and integrated gene set enrichment analysis to a joint visualization of data from all platforms in the context of metabolic or signalling pathways.
References
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