DiscoverySpace: an interactive data analysis application
Neil Robertson,Mehrdad Oveisi-Fordorei,Scott Zuyderduyn,Richard Varhol,Christopher D. Fjell,Marco A. Marra,Steven J.M. Jones,Asim Siddiqui +7 more
TL;DR: DiscoverySpace is a graphical application for bioinformatics data analysis that can seamlessly traverse references between biological databases and draw together annotations in an intuitive tabular interface.
read more
Abstract: DiscoverySpace is a graphical application for bioinformatics data analysis. Users can seamlessly traverse references between biological databases and draw together annotations in an intuitive tabular interface. Datasets can be compared using a suite of novel tools to aid in the identification of significant patterns. DiscoverySpace is of broad utility and its particular strength is in the analysis of serial analysis of gene expression (SAGE) data. The application is freely available online.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Molecular mechanisms of toxicity of silver nanoparticles in zebrafish embryos.
Ronny van Aerle,Anke Lange,Alex Moorhouse,Konrad Paszkiewicz,Katie Ball,Blair D. Johnston,Eliane S. R. De-Bastos,Timothy F. Booth,Charles R. Tyler,Eduarda M. Santos +9 more
TL;DR: The data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos and are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms.
239
•Proceedings Article
Integrating Biological Databases.
Carlos A. Heuser,Luiz Fernando Bessa Seibel,Eduardo Kroth +2 more
- 01 Jan 2003
211
Evolution of C4 photosynthesis in the genus Flaveria: how many and which genes does it take to make C4?
TL;DR: A comparative transcriptome analysis in leaves of five closely related C3, C4, and C3-C4 intermediate Flaveria species is carried out to gain insight into the extent to which gene expression patterns were altered in the evolutionary progression from C3 to C4.
210
Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns
Timothy F. Sharbel,Marie-Luise Voigt,José M. Corral,Giulio Galla,Jochen Kumlehn,Christian Klukas,Falk Schreiber,Falk Schreiber,Heiko Vogel,Björn Rotter +9 more
TL;DR: It is found that expression patterns of many reproduction genes, including an overabundance of regulatory factors, differ during sexual and asexual ovule development, thus providing a possible mechanism for inducing the complex reproductive changes required to generate clonal offspring.
143
An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans.
Barbara Meissner,Adam Warner,Kim Wong,Nicholas Dube,Adam Lorch,Sheldon J. McKay,Jaswinder Khattra,Teresa M. Rogalski,Aruna Somasiri,Iasha Chaudhry,Rebecca M. Fox,David M. Miller,David L. Baillie,Robert A. Holt,Steven J.M. Jones,Marco A. Marra,Donald G. Moerman +16 more
TL;DR: It is proposed that additional sarcomeric proteins exist for which there is a less severe, or entirely different, mutant phenotype produced in their absence from late embryonic muscle gene expression.
116
References
KEGG: Kyoto Encyclopedia of Genes and Genomes
Minoru Kanehisa,Susumu Goto +1 more
TL;DR: The Kyoto Encyclopedia of Genes and Genomes (KEGG) as discussed by the authors is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules.
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Pfam: the protein families database.
Robert D. Finn,Alex Bateman,Jody Clements,Penelope Coggill,Ruth Y. Eberhardt,Sean R. Eddy,Andreas Heger,Kirstie Hetherington,Liisa Holm,Jaina Mistry,Erik L. L. Sonnhammer,John Tate,Marco Punta +12 more
TL;DR: Pfam as discussed by the authors is a widely used database of protein families, containing 14 831 manually curated entries in the current version, version 27.0, and has been updated several times since 2012.
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
TL;DR: The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data and provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-power gene expression and genomic hybridization experiments.
13.2K
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Related Papers (5)
Jaswinder Khattra,Allen Delaney,Yongjun Zhao,Asim Siddiqui,Jennifer Asano,Helen McDonald,Pawan Pandoh,Noreen Dhalla,Anna-Liisa Prabhu,Kevin Ma,Stephanie Lee,Adrian Ally,Angela Tam,Danne Sa,Sean A Rogers,David L. Charest,Jeffrey L Stott,Scott Zuyderduyn,Richard Varhol,Connie J. Eaves,Steven J.M. Jones,Robert A. Holt,Martin Hirst,Pamela A. Hoodless,Marco A. Marra +24 more
Jeremy Schmutz,Steven B. Cannon,Jessica A. Schlueter,Jessica A. Schlueter,Jianxin Ma,Therese Mitros,William Nelson,David L. Hyten,Qijian Song,Qijian Song,Jay J. Thelen,Jianlin Cheng,Dong Xu,Uffe Hellsten,Gregory D. May,Yeisoo Yu,Tetsuya Sakurai,Taishi Umezawa,Madan K. Bhattacharyya,Devinder Sandhu,Babu Valliyodan,Erika Lindquist,Myron Peto,David Grant,Shengqiang Shu,David Goodstein,Kerrie Barry,Montona Futrell-Griggs,Brian Abernathy,Jianchang Du,Zhixi Tian,Liucun Zhu,Navdeep Gill,Trupti Joshi,Marc Libault,Ananad Sethuraman,Xue-Cheng Zhang,Kazuo Shinozaki,Henry T. Nguyen,Rod A. Wing,Perry B. Cregan,James E. Specht,Jane Grimwood,Daniel S. Rokhsar,Gary Stacey,Randy C. Shoemaker,Scott A. Jackson +46 more