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. 2003 Jul 1;31(13):3461-7.
doi: 10.1093/nar/gkg591.

GEPAS: A web-based resource for microarray gene expression data analysis

Javier Herrero  1 , Fátima Al-Shahrour, Ramón Díaz-Uriarte, Alvaro Mateos, Juan M Vaquerizas, Javier Santoyo, Joaquín Dopazo
Affiliations

GEPAS: A web-based resource for microarray gene expression data analysis

Javier Herrero et al. Nucleic Acids Res. .

Abstract

We present a web-based pipeline for microarray gene expression profile analysis, GEPAS, which stands for Gene Expression Profile Analysis Suite (http://gepas.bioinfo.cnio.es). GEPAS is composed of different interconnected modules which include tools for data pre-processing, two-conditions comparison, unsupervised and supervised clustering (which include some of the most popular methods as well as home made algorithms) and several tests for differential gene expression among different classes, continuous variables or survival analysis. A multiple purpose tool for data mining, based on Gene Ontology, is also linked to the tools, which constitutes a very convenient way of analysing clustering results. On-line tutorials are available from our main web server (http://bioinfo.cnio.es).

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Figures

Figure 1
Figure 1
The pipeline of microarray data analysis. After the operations of image processing and data normalisation are performed (grey box on top left), the data enters the pipeline through the preprocessor. Then, depending on the type of analysis the user needs to perform, these can be sent to different modules that implement different tools.
Figure 2
Figure 2
Representation provided by Pomelo of the 100 genes most differentially expressed among two different cancer types, acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) labelled as 0 and 1, respectively in the top of the figure. The genes are arranged in increasing order of adjusted p-value. If an adjusted p-value of 0.05 is used, there are 92 genes that present significant differential expression among the classes. Thermal scale in the bottom represents fold of activation or repression in log2 scale. Data from (25).
Figure 3
Figure 3
Use of SOTAarray and SotaTree modules. Arrows represent clicks for the user. (A) The interface to the SOTArray. (B) The results page, from which different plots can be obtained. (C) SOTA tree program was invoked from the results page. This graphical interface allows for some interactive changes in the final appearance of the tree represented. (D) A dendrogram representing the clusters found in the dataset. The diameter of the circle is proportional to the number of co-expressing genes in the cluster. By clicking the circle or the histogram representing the average profile, the list of genes (E) and a representation of its profiles (F), respectively, can be obtained. This is done by the internal module ExtractCluster. (G) Shows part of the graphical representation of FatiGO module, which displays the percentages of GO terms in the selected cluster with respect to the rest of genes and the adjusted p-values obtained for this difference.
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References

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