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. 2003 Jul 1;31(13):3471-6.
doi: 10.1093/nar/gkg629.

GenePublisher: Automated analysis of DNA microarray data

Steen Knudsen  1 , Christopher Workman, Thomas Sicheritz-Ponten, Carsten Friis
Affiliations

GenePublisher: Automated analysis of DNA microarray data

Steen Knudsen et al. Nucleic Acids Res. .

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.

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Figures

Figure 1
Figure 1
Overview of the GenePublisher system. The shell script calls all other programs and databases and coordinates their execution. The script reads a parameter file with user adjustable parameters and reads the data input. The script, in turn, can be called via a Makefile or via a web interface.
Figure 2
Figure 2
A list of all signal transduction pathways in which genes were found on the chip. The x-axis shows the unadjusted P-value of each gene assigned to each pathway. Low P-values indicate differential expression. Pathways with differential expression should stand out from the background level.
Figure 3
Figure 3
The cancernet pathway from TRANSPATH. The significantly regulated Fas receptor is found in the lower right corner of the cell.
Figure 4
Figure 4
A list of all KEGG pathways in which genes were found on the chip. The x-axis shows the unadjusted P-value of each gene assigned to each pathway. Low P-values indicate differential expression. Pathways with differential expression should stand out from the background level.
See this image and copyright information in PMC

References

    1. The Chipping Forecast II (2002) Nature Genet., 32.
    1. Liu G., Loraine,A.E., Shigeta,R., Cline,M., Cheng,J., Valmeekam,V., Sun,S., Kulp,D. and Siani-Rose,M.A. (2003) NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res., 31, 82–86. - PMC - PubMed
    1. Brazma A., Parkinson,H., Sarkans,U., Shojatalab,M., Vilo,J., Abeygunawardena,N., Holloway,E., Kapushesky,M., Kemmeren,P., Lara,G.G. et al. (2003) ArrayExpress—a public repository for microarray gene expression data at the EBI. Nucleic Acids Res., 31, 68–71. - PMC - PubMed
    1. Brazma A., Hingamp,P., Quackenbush,J., Sherlock,G., Spellman,P., Stoeckert,C., Aach,J., Ansorge,W., Ball,C.A., Causton,H.C. et al. (2001) Minimum information about a microarray experiment (MIAME)—toward standards for microarray data, Nature Genet., 29, 365–371. - PubMed
    1. Workman C., Jensen,L.J., Jarmer,H., Berka,R., Saxild,H.H., Gautier,L., Nielsen,C., Nielsen,H.B., Brunak,S. and Knudsen,S. (2002) A new non-linear method for reducing variance between DNA microarray experiments. Genome Biol., 3, research0048.1–0048.16. - PMC - PubMed

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