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
Reads0
Chats0
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
Citations
More filters
Book ChapterDOI
The Application of DamID to Identify Peripheral Gene Sequences in Differentiated and Primary Cells
TL;DR: A detailed methodology to adapt DamID to novel cell types, in particular differentiated cells in culture, and highlights heretofore largely ignored variations in the PCR amplified DNA products generated by the DamID procedure.
Journal ArticleDOI
Analysis of structure and gene expression of bovine CCDC3 gene indicates a function in fat metabolism.
Annett Eberlein,Claudia Kalbe,Tom Goldammer,Ronald M. Brunner,Christa Kuehn,Rosemarie Weikard +5 more
TL;DR: This first report of structural analysis and molecular characterization of the CCDC3 gene in cattle will contribute to a better understanding of the yet unknown physiological role of the respective protein in mammals.
Journal ArticleDOI
Selection against Robertsonian fusions involving housekeeping genes in the house mouse: integrating data from gene expression arrays and chromosome evolution
TL;DR: It is shown that the pericentromeric region of one such chromosome, MMU19, which is infrequently encountered as a fusion partner in wild populations, is significantly enriched for housekeeping genes when compared to other chromosomes in the genome, suggesting that there is selection against breakpoints in the percentromeric area.
Journal ArticleDOI
NLRC5 promotes transcription of BTN3A1-3 genes and Vγ9Vδ2 T cell-mediated killing.
Anh Thu Dang,Juliane Strietz,Alessandro Zenobi,Hanif Javanmard Khameneh,Simon M. Brandl,Laura Lozza,Gregor Conradt,Stefan H. E. Kaufmann,Stefan H. E. Kaufmann,Walter Reith,Ivo Kwee,Susana Minguet,Sonia T. Chelbi,Greta Guarda +13 more
TL;DR: It is shown that NLRC5 regulates the expression of BTN3A genes and hence open opportunities to modulate antimicrobial and anticancer immunity.
Journal ArticleDOI
Identification by Gene Coregulation Mapping of Novel Genes Involved in Embryonic Stem Cell Differentiation
Jeroen L. A. Pennings,Dorien A.M. van Dartel,Dorien A.M. van Dartel,Tessa E. Pronk,Tessa E. Pronk,Peter J.M. Hendriksen,Aldert H. Piersma,Aldert H. Piersma +7 more
TL;DR: This work takes literature gene sets derived from (supplementary) tables as input and uses gene co-occurrence in these sets for mapping a co-regulation network and identified 43 genes not previously associated with cardiac ESC differentiation for which a putative novel biological function is assigned.
References
More filters
Journal ArticleDOI
Most mammalian mRNAs are conserved targets of microRNAs
TL;DR: This work overhauled its tool for finding preferential conservation of sequence motifs and applied it to the analysis of human 3'UTRs, increasing by nearly threefold the detected number of preferentially conserved miRNA target sites.
Journal ArticleDOI
KEGG for linking genomes to life and the environment
Minoru Kanehisa,Michihiro Araki,Susumu Goto,Masahiro Hattori,Mika Hirakawa,Masumi Itoh,Toshiaki Katayama,Shuichi Kawashima,Shujiro Okuda,Toshiaki Tokimatsu,Yoshihiro Yamanishi +10 more
TL;DR: KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps, and the KEGG resource is being expanded to suit the needs for practical applications.
Journal ArticleDOI
Genome-wide atlas of gene expression in the adult mouse brain
Ed S. Lein,Michael Hawrylycz,Nancy Ao,Mikael Ayres,Amy Bensinger,Amy Bernard,Andrew F. Boe,Mark S. Boguski,Mark S. Boguski,Kevin S. Brockway,Emi J. Byrnes,Lin Chen,Li Chen,Tsuey-Ming Chen,Mei Chi Chin,Jimmy Chong,Brian E. Crook,Aneta Czaplinska,Chinh Dang,Suvro Datta,Nick Dee,Aimee L. Desaki,Tsega Desta,Ellen Diep,Tim A. Dolbeare,Matthew J. Donelan,Hong-Wei Dong,Jennifer G. Dougherty,Ben J. Duncan,Amanda Ebbert,Gregor Eichele,Lili K. Estin,Casey Faber,Benjamin A.C. Facer,Rick Fields,Shanna R. Fischer,Tim P. Fliss,Cliff Frensley,Sabrina N. Gates,Katie J. Glattfelder,Kevin R. Halverson,Matthew R. Hart,John G. Hohmann,Maureen P. Howell,Darren P. Jeung,Rebecca A. Johnson,Patrick T. Karr,Reena Kawal,Jolene Kidney,Rachel H. Knapik,Chihchau L. Kuan,James H. Lake,Annabel R. Laramee,Kirk D. Larsen,Christopher Lau,Tracy Lemon,Agnes J. Liang,Ying Liu,Lon T. Luong,Jesse Michaels,Judith J. Morgan,Rebecca J. Morgan,Marty Mortrud,Nerick Mosqueda,Lydia Ng,Randy Ng,Geralyn J. Orta,Caroline C. Overly,Tu H. Pak,Sheana Parry,Sayan Dev Pathak,Owen C. Pearson,Ralph B. Puchalski,Zackery L. Riley,Hannah R. Rockett,Stephen A. Rowland,Joshua J. Royall,Marcos J. Ruiz,Nadia R. Sarno,Katherine Schaffnit,Nadiya V. Shapovalova,Taz Sivisay,Clifford R. Slaughterbeck,Simon Smith,Kimberly A. Smith,Bryan I. Smith,Andy J. Sodt,Nick N. Stewart,Kenda-Ruth Stumpf,Susan M. Sunkin,Madhavi Sutram,Angelene Tam,Carey D. Teemer,Christina Thaller,Carol L. Thompson,Lee R. Varnam,Axel Visel,Axel Visel,Ray M. Whitlock,Paul Wohnoutka,Crissa K. Wolkey,Victoria Y. Wong,Matthew J.A. Wood,Murat B. Yaylaoglu,Rob Young,Brian L. Youngstrom,Xu Feng Yuan,Bin Zhang,Theresa A. Zwingman,Allan R. Jones +109 more
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.
Related Papers (5)
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more