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. 2004 Jul 1;32(Web Server issue):W465-70.
doi: 10.1093/nar/gkh470.

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

Misha Kapushesky  1 , Patrick Kemmeren, Aedín C Culhane, Steffen Durinck, Jan Ihmels, Christine Körner, Meelis Kull, Aurora Torrente, Ugis Sarkans, Jaak Vilo, Alvis Brazma
Affiliations

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

Misha Kapushesky et al. Nucleic Acids Res. .

Abstract

Expression Profiler (EP, http://www.ebi.ac.uk/expressionprofiler) is a web-based platform for microarray gene expression and other functional genomics-related data analysis. The new architecture, Expression Profiler: next generation (EP:NG), modularizes the original design and allows individual analysis-task-related components to be developed by different groups and yet still seamlessly to work together and share the same user interface look and feel. Data analysis components for gene expression data preprocessing, missing value imputation, filtering, clustering methods, visualization, significant gene finding, between group analysis and other statistical components are available from the EBI (European Bioinformatics Institute) web site. The web-based design of Expression Profiler supports data sharing and collaborative analysis in a secure environment. Developed tools are integrated with the microarray gene expression database ArrayExpress and form the exploratory analytical front-end to those data. EP:NG is an open-source project, encouraging broad distribution and further extensions from the scientific community.

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Figures

Figure 1
Figure 1
A typical analysis workflow. (A) After the user logs in, the data file is uploaded via the Data Upload component. (B) A subselection is made via the Data Selection component (the distribution histogram indicates the spread of the data and helps choose the range criteria). (C) Data Transformation is used to impute the missing values in the resulting data subset; clicking on the dataset name will return the new matrix with estimated missing values. (D) Hierarchical Clustering with tree collapsing is used to get the first overview of the data structure; (E) the hierarchical tree is displayed as an SVG image, allowing the user to zoom in on the tree in detail.
Figure 2
Figure 2
EP:NG system overview. All access is realized through the FRONT-END, which uses the Expression Profiler Component (EPC) description files to present a graphical user interface (GUI), and then sends the user's request to the CORE for either local execution on the Linux server farm at the EBI or remote processing on external (non-EBI) computer servers.
Figure 3
Figure 3
Similarity Search Visualization component. The user can select with the mouse a subset of conditions where the expression line-plot shows correlation by visual inspection. The chosen genes and conditions can be sent to other components for further analysis (e.g. to Data Selection).
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