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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Comprehensive comparison of large-scale tissue expression datasets
Alberto Santos,Kalliopi Tsafou,Christian Stolte,Sune Pletscher-Frankild,Seán I. O'Donoghue,Seán I. O'Donoghue,Lars Juhl Jensen +6 more
TL;DR: A comprehensive evaluation of tissue expression data from a variety of experimental techniques is presented and it is found that most datasets support the assumed but not demonstrated distinction between tissue-specific and ubiquitous expression.
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Selective loss of smaller spines in Schizophrenia
Matthew L. MacDonald,Jamil Alhassan,Jason T. Newman,Michelle Richard,Michelle Richard,Michelle Richard,Hong Gu,Hong Gu,Hong Gu,Ryan M. Kelly,Ryan M. Kelly,Ryan M. Kelly,Alan R. Sampson,Alan R. Sampson,Alan R. Sampson,Kenneth N. Fish,Kenneth N. Fish,Kenneth N. Fish,Peter Penzes,Zachary P. Wills,Zachary P. Wills,Zachary P. Wills,David A. Lewis,David A. Lewis,David A. Lewis,Robert A. Sweet,Robert A. Sweet,Robert A. Sweet +27 more
TL;DR: Findings require a rethinking of the overpruning hypothesis, demonstrate a link between small spine loss and a schizophrenia risk gene, and should spur more in-depth investigations of the mechanisms that govern new or small spine generation and stabilization under normal conditions as well as how this process is impaired in schizophrenia.
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PARP12, an Interferon-stimulated Gene Involved in the Control of Protein Translation and Inflammation
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References
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Journal ArticleDOI
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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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