Literature DB >> 17917127

Sharing and reusing gene expression profiling data in neuroscience.

Xiang Wan1, Paul Pavlidis.   

Abstract

As public availability of gene expression profiling data increases, it is natural to ask how these data can be used by neuroscientists. Here we review the public availability of high-throughput expression data in neuroscience and how it has been reused, and tools that have been developed to facilitate reuse. There is increasing interest in making expression data reuse a routine part of the neuroscience tool-kit, but there are a number of challenges. Data must become more readily available in public databases; efforts to encourage investigators to make data available are important, as is education on the benefits of public data release. Once released, data must be better-annotated. Techniques and tools for data reuse are also in need of improvement. Integration of expression profiling data with neuroscience-specific resources such as anatomical atlases will further increase the value of expression data.

Mesh:

Year:  2007        PMID: 17917127      PMCID: PMC2980754          DOI: 10.1007/s12021-007-0012-5

Source DB:  PubMed          Journal:  Neuroinformatics        ISSN: 1539-2791


  73 in total

1.  Expression Profiler: next generation--an online platform for analysis of microarray data.

Authors:  Misha Kapushesky; Patrick Kemmeren; Aedín C Culhane; Steffen Durinck; Jan Ihmels; Christine Körner; Meelis Kull; Aurora Torrente; Ugis Sarkans; Jaak Vilo; Alvis Brazma
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

2.  Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function.

Authors:  Elissa J Chesler; Lu Lu; Siming Shou; Yanhua Qu; Jing Gu; Jintao Wang; Hui Chen Hsu; John D Mountz; Nicole E Baldwin; Michael A Langston; David W Threadgill; Kenneth F Manly; Robert W Williams
Journal:  Nat Genet       Date:  2005-02-13       Impact factor: 38.330

3.  Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.

Authors:  T R Golub; D K Slonim; P Tamayo; C Huard; M Gaasenbeek; J P Mesirov; H Coller; M L Loh; J R Downing; M A Caligiuri; C D Bloomfield; E S Lander
Journal:  Science       Date:  1999-10-15       Impact factor: 47.728

4.  Comparison of microarray-based mRNA profiling technologies for identification of psychiatric disease and drug signatures.

Authors:  Linda W Jurata; Yury V Bukhman; Vinod Charles; Frank Capriglione; Jeffrey Bullard; Andrew L Lemire; Ali Mohammed; Quyen Pham; Pascal Laeng; Jeffrey A Brockman; C Anthony Altar
Journal:  J Neurosci Methods       Date:  2004-09-30       Impact factor: 2.390

5.  Cluster analysis and display of genome-wide expression patterns.

Authors:  M B Eisen; P T Spellman; P O Brown; D Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  1998-12-08       Impact factor: 11.205

6.  Bioconductor: open software development for computational biology and bioinformatics.

Authors:  Robert C Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Marcel Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael Irizarry; Friedrich Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang
Journal:  Genome Biol       Date:  2004-09-15       Impact factor: 13.583

7.  Expression of HSPF1 and LIM in the lymphoblastoid cells derived from patients with bipolar disorder and schizophrenia.

Authors:  Kazuya Iwamoto; Miki Bundo; Shinsuke Washizuka; Chihiro Kakiuchi; Tadafumi Kato
Journal:  J Hum Genet       Date:  2004       Impact factor: 3.172

8.  Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments.

Authors:  Rainer Breitling; Patrick Armengaud; Anna Amtmann; Pawel Herzyk
Journal:  FEBS Lett       Date:  2004-08-27       Impact factor: 4.124

9.  Further statistical analysis for genome-wide expression evolution in primate brain/liver/fibroblast tissues.

Authors:  Jianying Gu; Xun Gu
Journal:  Hum Genomics       Date:  2004-05       Impact factor: 4.639

10.  The functional landscape of mouse gene expression.

Authors:  Wen Zhang; Quaid D Morris; Richard Chang; Ofer Shai; Malina A Bakowski; Nicholas Mitsakakis; Naveed Mohammad; Mark D Robinson; Ralph Zirngibl; Eszter Somogyi; Nancy Laurin; Eftekhar Eftekharpour; Eric Sat; Jörg Grigull; Qun Pan; Wen-Tao Peng; Nevan Krogan; Jack Greenblatt; Michael Fehlings; Derek van der Kooy; Jane Aubin; Benoit G Bruneau; Janet Rossant; Benjamin J Blencowe; Brendan J Frey; Timothy R Hughes
Journal:  J Biol       Date:  2004-12-06
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  4 in total

Review 1.  Data publishing and scientific journals: the future of the scientific paper in a world of shared data.

Authors:  Erik De Schutter
Journal:  Neuroinformatics       Date:  2010-10

Review 2.  Quantitative investigations of axonal and dendritic arbors: development, structure, function, and pathology.

Authors:  Ruchi Parekh; Giorgio A Ascoli
Journal:  Neuroscientist       Date:  2014-06-27       Impact factor: 7.519

3.  Data reuse and the open data citation advantage.

Authors:  Heather A Piwowar; Todd J Vision
Journal:  PeerJ       Date:  2013-10-01       Impact factor: 2.984

4.  Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation.

Authors:  Hannah Gelman; Jennifer N Dines; Jonathan Berg; Alice H Berger; Sarah Brnich; Fuki M Hisama; Richard G James; Alan F Rubin; Jay Shendure; Brian Shirts; Douglas M Fowler; Lea M Starita
Journal:  Genome Med       Date:  2019-12-20       Impact factor: 11.117

  4 in total

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