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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BioGPS: building your own mash-up of gene annotations and expression profiles
TL;DR: This article focuses on the updates to BioGPS since the last paper, which updated the most popular plugin, the ‘Gene expression/activity chart’, to include ∼6000 datasets (from ∼2000 datasets) and enhanced user interactivity.
Journal ArticleDOI
BioGPS and MyGene.info: organizing online, gene-centric information
TL;DR: This article describes updates to BioGPS made after its initial release in 2008, and summarizes recent additions of features and data, as well as the robust user activity that underlies this community intelligence application.
Journal ArticleDOI
DGIdb 2.0: mining clinically relevant drug-gene interactions.
Alex H. Wagner,Adam C. Coffman,Benjamin J. Ainscough,Nicholas C. Spies,Zachary L. Skidmore,Katie M. Campbell,Kilannin Krysiak,Deng Pan,Joshua F. McMichael,James M. Eldred,Jason Walker,Rick K. Wilson,Elaine R. Mardis,Malachi Griffith,Obi L. Griffith +14 more
TL;DR: Substantial updates have been made to increase content and improve its usefulness as a resource for mining clinically actionable drug targets, and a new web view and API have been developed to allow searching for interactions by drug identifiers to complement existing gene-based search functionality.
Journal ArticleDOI
Fate Mapping via Ms4a3-Expression History Traces Monocyte-Derived Cells.
Zhaoyuan Liu,Yaqi Gu,Svetoslav Chakarov,Camille Blériot,Immanuel Kwok,Xin Chen,Amanda Shin,Weijie Huang,Regine J. Dress,Charles-Antoine Dutertre,Andreas Schlitzer,Jinmiao Chen,Lai Guan Ng,Honglin Wang,Zhiduo Liu,Bing Su,Florent Ginhoux,Florent Ginhoux,Florent Ginhoux +18 more
TL;DR: The unambiguous identification of monocyte-derived cells will permit future studies of their function under any condition and precisely quantified the contribution of monocytes to the RTM pool during homeostasis and inflammation.
Journal ArticleDOI
Decoding myofibroblast origins in human kidney fibrosis
Christoph Kuppe,Mahmoud M. Ibrahim,Mahmoud M. Ibrahim,Jennifer Kranz,Jennifer Kranz,Xiaoting Zhang,Susanne Ziegler,Javier Perales-Patón,Javier Perales-Patón,Jitske Jansen,Jitske Jansen,Jitske Jansen,Katharina C Reimer,James R Smith,Ross Dobie,John R. Wilson-Kanamori,Maurice Halder,Yaoxian Xu,Nazanin Kabgani,Nadine Kaesler,Martin Klaus,Lukas Gernhold,Victor G. Puelles,Victor G. Puelles,Tobias B. Huber,Peter Boor,Sylvia Menzel,Remco Hoogenboezem,Eric Bindels,Joachim Steffens,Jürgen Floege,Rebekka K. Schneider,Rebekka K. Schneider,Julio Saez-Rodriguez,Julio Saez-Rodriguez,Julio Saez-Rodriguez,Neil C. Henderson,Rafael Kramann,Rafael Kramann +38 more
TL;DR: Using single-cell RNA sequencing, the transcriptomes of cells from the proximal and non-proximal tubules of healthy and fibrotic human kidneys are profiled to map the entire human kidney and identify distinct subpopulations of pericytes and fibroblasts as the main cellular sources of scar-forming myofibro Blasts during human kidney fibrosis.
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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.
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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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