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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Human genetic variation database, a reference database of genetic variations in the Japanese population.
Koichiro Higasa,Noriko Miyake,Jun Yoshimura,Kohji Okamura,Tetsuya Niihori,Hirotomo Saitsu,Koichiro Doi,Masakazu Shimizu,Kazuhiko Nakabayashi,Yoko Aoki,Yoshinori Tsurusaki,Shinichi Morishita,Takahisa Kawaguchi,Osuke Migita,Keiko Nakayama,Mitsuko Nakashima,Jun Mitsui,Maiko Narahara,Keiko Hayashi,Ryo Funayama,Daisuke Yamaguchi,Hiroyuki Ishiura,Wen Ya Ko,Wen Ya Ko,Kenichiro Hata,Takeshi Nagashima,Ryo Yamada,Yoichi Matsubara,Akihiro Umezawa,Shoji Tsuji,Naomichi Matsumoto,Fumihiko Matsuda +31 more
TL;DR: The results illustrate the importance of constructing an ethnicity-specific reference genome for identifying rare variants and constructed a Japanese-specific major allele reference genome, by which the number of unique mapping of the short reads in the data has increased 0.045% on average.
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Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.
TL;DR: A genome-wide mapping study of loci that are associated with functional variation in immune response to Mycobacterium tuberculosis identified a number of candidate loci, including the MAPK phosphatase DUSP14 in particular, that are promising susceptibility genes to pulmonary TB.
Journal ArticleDOI
Cooperative interaction between retinoic acid receptor-α and estrogen receptor in breast cancer
Caryn S. Ross-Innes,Rory Stark,Kelly A. Holmes,Dominic Schmidt,Christiana Spyrou,Roslin Russell,Charles E. Massie,Sarah L. Vowler,Matthew D. Eldridge,Jason S. Carroll +9 more
TL;DR: It is shown, on a genome-wide scale, that RAR alpha and ER can co-occupy regulatory regions together within the chromatin and suggest that different nuclear receptors can cooperate for effective transcriptional activity in breast cancer cells.
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Spatial encoding of cyclic AMP signaling specificity by GPCR endocytosis
TL;DR: In this paper, β2-adrenergic receptor-mediated cAMP signaling from internal compartments is more effective compared to the plasma membrane in regulating a distinct set of genes, demonstrating a functional significance for the spatial separation of cAMP signalling.
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A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.
Athma A. Pai,Jordana T. Bell,John C. Marioni,Jonathan K. Pritchard,Jonathan K. Pritchard,Yoav Gilad +5 more
TL;DR: It is estimated that, in the tissues studied, inter-species differences in promoter methylation might underlie as much as 12%–18% of differences in gene expression levels between humans and chimpanzees.
References
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