Literature DB >> 12824347

GenePublisher: Automated analysis of DNA microarray data.

Steen Knudsen1, Christopher Workman, Thomas Sicheritz-Ponten, Carsten Friis.   

Abstract

GenePublisher, a system for automatic analysis of data from DNA microarray experiments, has been implemented with a web interface at http://www.cbs.dtu.dk/services/GenePublisher. Raw data are uploaded to the server together with a specification of the data. The server performs normalization, statistical analysis and visualization of the data. The results are run against databases of signal transduction pathways, metabolic pathways and promoter sequences in order to extract more information. The results of the entire analysis are summarized in report form and returned to the user.

Mesh：

Year:  2003        PMID： 12824347      PMCID： PMC169191          DOI： 10.1093/nar/gkg629

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  16 in total

1.  Validating clustering for gene expression data.

Authors:  K Y Yeung; D R Haynor; W L Ruzzo
Journal:  Bioinformatics       Date:  2001-04       Impact factor: 6.937

2.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

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

3.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

4.  Correspondence analysis applied to microarray data.

Authors:  K Fellenberg; N C Hauser; B Brors; A Neutzner; J D Hoheisel; M Vingron
Journal:  Proc Natl Acad Sci U S A       Date:  2001-09-04       Impact factor: 11.205

5.  The KEGG databases at GenomeNet.

Authors:  Minoru Kanehisa; Susumu Goto; Shuichi Kawashima; Akihiro Nakaya
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

6.  The Ensembl genome database project.

Authors:  T Hubbard; D Barker; E Birney; G Cameron; Y Chen; L Clark; T Cox; J Cuff; V Curwen; T Down; R Durbin; E Eyras; J Gilbert; M Hammond; L Huminiecki; A Kasprzyk; H Lehvaslaiho; P Lijnzaad; C Melsopp; E Mongin; R Pettett; M Pocock; S Potter; A Rust; E Schmidt; S Searle; G Slater; J Smith; W Spooner; A Stabenau; J Stalker; E Stupka; A Ureta-Vidal; I Vastrik; M Clamp
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

7.  Prediction of human protein function from post-translational modifications and localization features.

Authors:  L J Jensen; R Gupta; N Blom; D Devos; J Tamames; C Kesmir; H Nielsen; H H Staerfeldt; K Rapacki; C Workman; C A F Andersen; S Knudsen; A Krogh; A Valencia; S Brunak
Journal:  J Mol Biol       Date:  2002-06-21       Impact factor: 5.469

8.  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

9.  Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection.

Authors:  C Li; W H Wong
Journal:  Proc Natl Acad Sci U S A       Date:  2001-01-02       Impact factor: 11.205

10.  A new non-linear normalization method for reducing variability in DNA microarray experiments.

Authors:  Christopher Workman; Lars Juhl Jensen; Hanne Jarmer; Randy Berka; Laurent Gautier; Henrik Bjørn Nielser; Hans-Henrik Saxild; Claus Nielsen; Søren Brunak; Steen Knudsen
Journal:  Genome Biol       Date:  2002-08-30       Impact factor: 13.583
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  14 in total

1.  ArrayPipe: a flexible processing pipeline for microarray data.

Authors:  Karsten Hokamp; Fiona M Roche; Michael Acab; Marc-Etienne Rousseau; Byron Kuo; David Goode; Dana Aeschliman; Jenny Bryan; Lorne A Babiuk; Robert E W Hancock; Fiona S L Brinkman
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

2.  Genes of Escherichia coli O157:H7 that are involved in high-pressure resistance.

Authors:  Aaron S Malone; Yoon-Kyung Chung; Ahmed E Yousef
Journal:  Appl Environ Microbiol       Date:  2006-04       Impact factor: 4.792

3.  Comparative gene expression profile of mouse carotid body and adrenal medulla under physiological hypoxia.

Authors:  M D Ganfornina; M T Pérez-García; G Gutiérrez; E Miguel-Velado; J R López-López; A Marín; D Sánchez; C González
Journal:  J Physiol       Date:  2005-05-12       Impact factor: 5.182

4.  AMDA: an R package for the automated microarray data analysis.

Authors:  Mattia Pelizzola; Norman Pavelka; Maria Foti; Paola Ricciardi-Castagnoli
Journal:  BMC Bioinformatics       Date:  2006-07-06       Impact factor: 3.169

5.  Robust computational reconstitution - a new method for the comparative analysis of gene expression in tissues and isolated cell fractions.

Authors:  Martin Hoffmann; Dirk Pohlers; Dirk Koczan; Hans-Jürgen Thiesen; Stefan Wölfl; Raimund W Kinne
Journal:  BMC Bioinformatics       Date:  2006-08-04       Impact factor: 3.169

6.  MAGMA: analysis of two-channel microarrays made easy.

Authors:  Hubert Rehrauer; Stefan Zoller; Ralph Schlapbach
Journal:  Nucleic Acids Res       Date:  2007-05-21       Impact factor: 16.971

7.  The bag or the spindle: the cell factory at the time of systems' biology.

Authors:  Antoine Danchin
Journal:  Microb Cell Fact       Date:  2004-11-10       Impact factor: 5.328

8.  Pomelo II: finding differentially expressed genes.

Authors:  Edward R Morrissey; Ramón Diaz-Uriarte
Journal:  Nucleic Acids Res       Date:  2009-05-12       Impact factor: 16.971

9.  Normalization and gene p-value estimation: issues in microarray data processing.

Authors:  Katrin Fundel; Robert Küffner; Thomas Aigner; Ralf Zimmer
Journal:  Bioinform Biol Insights       Date:  2008-05-28

10.  Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.

Authors:  Peter Li; Juan I Castrillo; Giles Velarde; Ingo Wassink; Stian Soiland-Reyes; Stuart Owen; David Withers; Tom Oinn; Matthew R Pocock; Carole A Goble; Stephen G Oliver; Douglas B Kell
Journal:  BMC Bioinformatics       Date:  2008-08-07       Impact factor: 3.169
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