Literature DB >> 22782548

Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data.

Anton Zoubarev1, Kelsey M Hamer, Kiran D Keshav, E Luke McCarthy, Joseph Roy C Santos, Thea Van Rossum, Cameron McDonald, Adam Hall, Xiang Wan, Raymond Lim, Jesse Gillis, Paul Pavlidis.   

Abstract

UNLABELLED: Gemma is a database, analysis software system and web site for genomics data re-use and meta-analysis. Currently, Gemma contains analyzed data from over 3300 expression profiling studies, yielding hundreds of millions of differential expression results and coexpression patterns (correlated expression) for retrieval and visualization. With optional registration users can save their own data and securely share it with other users. Web services and integration with third-party resources further increase the scope of the tools, which include a Cytoscape plugin. AVAILABILITY: http://chibi.ubc.ca/Gemma, Apache 2.0 license.

Mesh：

Year:  2012        PMID： 22782548      PMCID： PMC3426847          DOI： 10.1093/bioinformatics/bts430

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  12 in total

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Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  Coexpression analysis of human genes across many microarray data sets.

Authors:  Homin K Lee; Amy K Hsu; Jon Sajdak; Jie Qin; Paul Pavlidis
Journal:  Genome Res       Date:  2004-06       Impact factor: 9.043

3.  Cytoscape: software for visualization and analysis of biological networks.

Authors:  Michael Kohl; Sebastian Wiese; Bettina Warscheid
Journal:  Methods Mol Biol       Date:  2011

4.  Application and evaluation of automated semantic annotation of gene expression experiments.

Authors:  Leon French; Suzanne Lane; Tamryn Law; Lydia Xu; Paul Pavlidis
Journal:  Bioinformatics       Date:  2009-04-17       Impact factor: 6.937

5.  Cytoscape Web: an interactive web-based network browser.

Authors:  Christian T Lopes; Max Franz; Farzana Kazi; Sylva L Donaldson; Quaid Morris; Gary D Bader
Journal:  Bioinformatics       Date:  2010-07-23       Impact factor: 6.937

6.  The impact of multifunctional genes on "guilt by association" analysis.

Authors:  Jesse Gillis; Paul Pavlidis
Journal:  PLoS One       Date:  2011-02-18       Impact factor: 3.240

7.  Disease Ontology: a backbone for disease semantic integration.

Authors:  Lynn Marie Schriml; Cesar Arze; Suvarna Nadendla; Yu-Wei Wayne Chang; Mark Mazaitis; Victor Felix; Gang Feng; Warren Alden Kibbe
Journal:  Nucleic Acids Res       Date:  2011-11-12       Impact factor: 16.971

8.  Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms.

Authors:  Michael Barnes; Johannes Freudenberg; Susan Thompson; Bruce Aronow; Paul Pavlidis
Journal:  Nucleic Acids Res       Date:  2005-10-19       Impact factor: 16.971

9.  NCBI GEO: mining tens of millions of expression profiles--database and tools update.

Authors:  Tanya Barrett; Dennis B Troup; Stephen E Wilhite; Pierre Ledoux; Dmitry Rudnev; Carlos Evangelista; Irene F Kim; Alexandra Soboleva; Maxim Tomashevsky; Ron Edgar
Journal:  Nucleic Acids Res       Date:  2006-11-11       Impact factor: 16.971

10.  Analysis of strain and regional variation in gene expression in mouse brain.

Authors:  P Pavlidis; W S Noble
Journal:  Genome Biol       Date:  2001-09-27       Impact factor: 13.583
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  54 in total

1.  A transcriptional signature of hub connectivity in the mouse connectome.

Authors:  Ben D Fulcher; Alex Fornito
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2.  Meta-Analysis of Gene Expression in Autism Spectrum Disorder.

Authors:  Carolyn Ch'ng; Willie Kwok; Sanja Rogic; Paul Pavlidis
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3.  Network-based metaanalysis identifies HNF4A and PTBP1 as longitudinally dynamic biomarkers for Parkinson's disease.

Authors:  Jose A Santiago; Judith A Potashkin
Journal:  Proc Natl Acad Sci U S A       Date:  2015-02-02       Impact factor: 11.205

4.  Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement.

Authors:  Ibrahim Burak Ozyurt; Jeffrey S Grethe
Journal:  Database (Oxford)       Date:  2018-01-01       Impact factor: 3.451

5.  Transcriptomic Evidence for Alterations in Astrocytes and Parvalbumin Interneurons in Subjects With Bipolar Disorder and Schizophrenia.

Authors:  Lilah Toker; Burak Ogan Mancarci; Shreejoy Tripathy; Paul Pavlidis
Journal:  Biol Psychiatry       Date:  2018-07-21       Impact factor: 13.382

6.  Meta-Analysis of Gene Expression Patterns in Animal Models of Prenatal Alcohol Exposure Suggests Role for Protein Synthesis Inhibition and Chromatin Remodeling.

Authors:  Sanja Rogic; Albertina Wong; Paul Pavlidis
Journal:  Alcohol Clin Exp Res       Date:  2016-03-20       Impact factor: 3.455

7.  An integrative modeling framework reveals plasticity of TGF-β signaling.

Authors:  Geoffroy Andrieux; Michel Le Borgne; Nathalie Théret
Journal:  BMC Syst Biol       Date:  2014-03-12

8.  Interactive Exploration, Analysis, and Visualization of Complex Phenome-Genome Datasets with ASPIREdb.

Authors:  Powell Patrick Cheng Tan; Sanja Rogic; Anton Zoubarev; Cameron McDonald; Frances Lui; Gayathiri Charathsandran; Matthew Jacobson; Manuel Belmadani; Justin Leong; Thea Van Rossum; Elodie Portales-Casamar; Ying Qiao; Kristina Calli; Xudong Liu; Melissa Hudson; Evica Rajcan-Separovic; Me Suzanne Lewis; Paul Pavlidis
Journal:  Hum Mutat       Date:  2016-05-20       Impact factor: 4.878

9.  Correlated Gene Expression and Anatomical Communication Support Synchronized Brain Activity in the Mouse Functional Connectome.

Authors:  Brian D Mills; David S Grayson; Anandakumar Shunmugavel; Oscar Miranda-Dominguez; Eric Feczko; Eric Earl; Kim A Neve; Damien A Fair
Journal:  J Neurosci       Date:  2018-05-22       Impact factor: 6.167

10.  Semantic Web repositories for genomics data using the eXframe platform.

Authors:  Emily Merrill; Stéphane Corlosquet; Paolo Ciccarese; Tim Clark; Sudeshna Das
Journal:  J Biomed Semantics       Date:  2014-06-03
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