BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.
Chunlei Wu,Camilo Orozco,Jason Boyer,Marc Leglise,James Goodale,Serge Batalov,Christopher L Hodge,James Haase,Jeff Janes,Jon W. Huss,Andrew I. Su +10 more
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TLDR
BioGPS http://biogps.gnf.org is introduced, a centralized gene portal for aggregating distributed gene annotation resources, and embraces the principle of community intelligence, enabling any user to easily and directly contribute to the BioGPS platform.Abstract:
Online gene annotation resources are indispensable for analysis of genomics data. However, the landscape of these online resources is highly fragmented, and scientists often visit dozens of these sites for each gene in a candidate gene list. Here, we introduce BioGPS http://biogps.gnf.org, a centralized gene portal for aggregating distributed gene annotation resources. Moreover, BioGPS embraces the principle of community intelligence, enabling any user to easily and directly contribute to the BioGPS platform.read more
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Missense mutations in TENM4, a regulator of axon guidance and central myelination, cause essential tremor
Hyun Hor,Ludmila Francescatto,Luca Bartesaghi,Luca Bartesaghi,Sara Ortega-Cubero,Maria Kousi,Oswaldo Lorenzo-Betancor,Félix Javier Jiménez-Jiménez,Alexandre Gironell,Jordi Clarimón,Oliver Drechsel,José A. G. Agúndez,Daniela Kenzelmann Broz,Ruth Chiquet-Ehrismann,Alberto Lleó,F. Coria,Elena García-Martín,Hortensia Alonso-Navarro,María José Martí,Jaume Kulisevsky,Jaume Kulisevsky,Charlotte N. Hor,Stephan Ossowski,Roman Chrast,Roman Chrast,Nicholas Katsanis,Pau Pastor,Xavier Estivill +27 more
TL;DR: The genetic and functional data, corroborated by the existence of a Tenm4 knockout mouse displaying an ET phenotype, implicates TENM4 in ET and intimate that processes regulating myelination in the central nervous system and axon guidance might be significant contributors to the genetic burden of this disorder.
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Diversity Outbred Mice Identify Population-Based Exposure Thresholds and Genetic Factors that Influence Benzene-Induced Genotoxicity.
John E. French,Daniel M. Gatti,Daniel L. Morgan,Grace E. Kissling,Keith R. Shockley,Gabriel A. Knudsen,Kim G. Shepard,Herman C. Price,Deborah King,Kristine L. Witt,Lars C. Pedersen,Steven C. Munger,Karen L. Svenson,Gary A. Churchill +13 more
TL;DR: The identification of sulfotransferases as candidate genes suggests that DO mice may provide additional insight into benzene-induced genotoxicity, and the genetically diverse DO mice provided a reproducible response to benzene exposure.
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Calling in SYK: SYK's dual role as a tumor promoter and tumor suppressor in cancer.
TL;DR: In cancers of non-immune cells, SYK provides a pro-survival signal, but can also suppress tumorigenesis by restricting epithelial-mesenchymal transition, enhancing cell-cell interactions and inhibiting migration.
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A role for PVRL4-driven cell–cell interactions in tumorigenesis
Natalya N. Pavlova,Natalya N. Pavlova,Christian P. Pallasch,Andrew E. H. Elia,Andrew E. H. Elia,Christian Braun,Thomas F. Westbrook,Michael T. Hemann,Stephen J. Elledge,Stephen J. Elledge +9 more
TL;DR: Pavlova et al. as discussed by the authors found that the poliovirus receptor-like 4 (PVRL4) allows attachment-free cell growth and also makes cells cluster together once detached from the extracellular matrix.
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MERAV: a tool for comparing gene expression across human tissues and cell types
Yoav D. Shaul,Bingbing Yuan,Prathapan Thiru,Andy Nutter-Upham,Scott McCallum,Carolyn Lanzkron,George W. Bell,David M. Sabatini +7 more
TL;DR: The Metabolic gEne RApid Visualizer (MERAV, http://merav.mit.edu), a web-based tool that can query a database comprising ∼4300 microarrays, representing human gene expression in normal tissues, cancer cell lines and primary tumors, is presented.
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TL;DR: An anatomically comprehensive digital atlas containing the expression patterns of ∼20,000 genes in the adult mouse brain is described, providing an open, primary data resource for a wide variety of further studies concerning brain organization and function.
Journal ArticleDOI
A gene atlas of the mouse and human protein-encoding transcriptomes
Andrew I. Su,Tim Wiltshire,Serge Batalov,Hilmar Lapp,Keith A. Ching,David Block,Jie Zhang,Richard Soden,Mimi Hayakawa,Gabriel Kreiman,Gabriel Kreiman,Michael P. Cooke,John R. Walker,John B. Hogenesch,John B. Hogenesch +14 more
TL;DR: In this paper, high-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale, and the authors have designed custom arrays that interrogate the expression of the vast majority of proteinencoding human and mouse genes and have used them to profile a panel of 79 human and 61 mouse tissues.
Journal ArticleDOI
STRING 8—a global view on proteins and their functional interactions in 630 organisms
Lars Juhl Jensen,Michael Kuhn,Manuel Stark,Samuel Chaffron,Christopher J. Creevey,Jean Muller,T. Doerks,Philippe Julien,Alexander Roth,Milan Simonovic,Peer Bork,Christian von Mering +11 more
TL;DR: The most important new developments in STRING 8 over previous releases include a URL-based programming interface, improved interaction prediction via genomic neighborhood in prokaryotes, and the inclusion of protein structures.
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