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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Dissertation
Pairwise rational kernels applied to metabolic network predictions
TL;DR: Rational kernels are based on transducers to manipulate sequence data, computing similarity measures between sequences or automata, and take advantage of the smaller and faster representation and algorithms of weighted finite-state transducers.
DissertationDOI
Bioinformatics Tools for the Analysis of Gene-Phenotype Relationships Coupled with a Next Generation ChIP-Sequencing Data Analysis Pipeline
TL;DR: A gene prioritization algorithm linking genes to non-disease phenotypes described by meaningful keywords was developed and can be used to process candidate genetic targets of a transcription factor produced by a computational pipeline for ChIP-Seq data analysis.
The mitotic genome: Accessibility and transcriptional control
TL;DR: The results obtained from measuring the sensitivity of chromatin to DNase I cleavage by sequencing (DNase-seq) in pure mitotic cell populations demonstrate that macromolecular accessibility of the mitotic genome is widely preserved, and raise important considerations for the commonly proposed “mitotic bookmark” hypothesis of transcriptional memory.
Journal ArticleDOI
bcGST-an interactive bias-correction method to identify over-represented gene-sets in boutique arrays.
Kevin Wang,Alexander M. Menzies,Alexander M. Menzies,Ines Pires da Silva,James S. Wilmott,Yibing Yan,Matthew Wongchenko,Richard F. Kefford,Richard A. Scolyer,Richard A. Scolyer,Georgina V. Long,Georgina V. Long,Garth Tarr,Samuel Mueller,Jean Yee Hwa Yang +14 more
TL;DR: The bcGST as discussed by the authors is a bias-corrected Gene Set Test (GST) method that introduces bias correction terms in the contingency table needed for calculating the Fisher's Exact Test.
Journal ArticleDOI
Human Protein Structural Interaction Network: Domain Effects on Network Topology and Protein Function*: Human Protein Structural Interaction Network: Domain Effects on Network Topology and Protein Function*
Lina Chen,Qian Wang,Yukui Shang,Liangcai Zhang,Zhao Sun,Wei-Ming He,Yan Zhao,Wan Li,Hong Wang,Yue-Han He,Xia Li +10 more
TL;DR: Human protein structural interaction network could exploit domain information to provide additional and crucial protein interaction details necessary for understanding what human structural interactions imply.
References
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Journal ArticleDOI
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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.
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Myles Hollander,Douglas A. Wolfe +1 more
TL;DR: An ideal text for an upper-level undergraduate or first-year graduate course, Nonparametric Statistical Methods, Second Edition is also an invaluable source for professionals who want to keep abreast of the latest developments within this dynamic branch of modern statistics.
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NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
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