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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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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The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Damian Szklarczyk,Andrea Franceschini,Michael Kuhn,Milan Simonovic,Alexander Roth,Pablo Minguez,Tobias Doerks,Manuel Stark,Jean Muller,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: An update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING), which provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information.
Journal ArticleDOI
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics
Linn Fagerberg,Björn M. Hallström,Per Oksvold,Caroline Kampf,Dijana Djureinovic,Jacob Odeberg,Masato Habuka,Simin Tahmasebpoor,Angelika Danielsson,Karolina Edlund,Anna Asplund,Evelina Sjöstedt,Emma Lundberg,Cristina Al-Khalili Szigyarto,Marie Skogs,Jenny Ottosson Takanen,Holger Berling,Hanna Tegel,Jan Mulder,Peter Nilsson,Jochen M. Schwenk,Cecilia Lindskog,Frida Danielsson,Adil Mardinoglu,Åsa Sivertsson,Kalle von Feilitzen,Mattias Forsberg,Martin Zwahlen,IngMarie Olsson,Sanjay Navani,Mikael Huss,Jens Nielsen,Jens Nielsen,Fredrik Pontén,Mathias Uhlén +34 more
TL;DR: A quantitative transcriptomics analysis (RNA-Seq) is used to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues.
Journal ArticleDOI
The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses
Gil Stelzer,Naomi Rosen,Inbar Plaschkes,Shahar Zimmerman,Michal Twik,Simon Fishilevich,Tsippi Iny Stein,Ron Nudel,Iris Lieder,Yaron Mazor,Sergey Kaplan,Dvir Dahary,David Warshawsky,Yaron Guan-Golan,Asher Kohn,Noa Rappaport,Marilyn Safran,Doron Lancet +17 more
TL;DR: GeneCards, the human gene compendium, enables researchers to effectively navigate and inter‐relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways and provides a stronger foundation for the GeneCards suite of companion databases and analysis tools.
Mediator and cohesin connect gene expression and chromatin architecture
Michael H. Kagey,Jamie J. Newman,Steve Bilodeau,Ye Zhan,David A. Orlando,Nynke L. van Berkum,Christopher C. Ebmeier,Jesse Goossens,Peter B. Rahl,Stuart S. Levine,Dylan J. Taatjes,Job Dekker,Richard A. Young +12 more
TL;DR: It is reported that mediator and cohesin physically and functionally connect the enhancers and core promoters of active genes in murine embryonic stem cells.
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Reactome: a database of reactions, pathways and biological processes
David Croft,Gavin O'Kelly,Guanming Wu,Robin Haw,Marc Gillespie,Lisa Matthews,Michael Caudy,Phani V. Garapati,Gopal R. Gopinath,Bijay Jassal,S Jupe,Irina Kalatskaya,Shahana S. Mahajan,Shahana S. Mahajan,Bruce May,Nelson Ndegwa,Esther Schmidt,Veronica Shamovsky,Christina K. Yung,Ewan Birney,Henning Hermjakob,Peter D'Eustachio,Lincoln Stein,Lincoln Stein,Lincoln Stein +24 more
TL;DR: A new web site with improved tools for pathway browsing and data analysis is developed, and orthology-based inferences of pathways in non-human species are made, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species.
References
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