Open Access Research article

Defining new criteria for selection of cell-based intestinal models using publicly available databases

Jon Christensen1, Sara El-Gebali2, Manuela Natoli3, Thierry Sengstag4, Mauro Delorenzi56, Susanne Bentz27, Hanifa Bouzourene8, Martin Rumbo9, Armando Felsani3, Sanna Siissalo10, Jouni Hirvonen10, Maya R Vila11, Piercarlo Saletti12, Michel Aguet136 and Pascale Anderle142567*

Author Affiliations

1 Institute for Macromolecular Chemistry and Center for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg, Germany

2 Institute of Biochemistry and Molecular Medicine, University of Berne, Berne, Switzerland

3 Istituto di Biologia Cellulare e Neurobiologia, CNR, Rome, Italy

4 OSC - Omics Science Center, RIKEN Yokohama Institute, Yokohama, Japan

5 Swiss Institute of Bioinformatics, Lausanne, Switzerland

6 Swiss National Centre of Competence in Research Molecular Oncology, Swiss Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Lausanne, Switzerland

7 NCCR TransCure, University of Berne, Berne, Switzerland

8 Institute of pathology of Lausanne, Centre hospitalier et universitaire vaudois, Lausanne, Switzerland

9 Laboratorio de Investigaciones del Sistema Inmune (LISIN), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina

10 Faculty of Pharmacy, University of Helsinki, Helsinki, Finland

11 LEITAT Technological Center, Barcelona, Spain

12 Medical Oncology Department, IOSI, Ospedale Regionale di Lugano, Lugano, Switzerland

13 Swiss Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Lausanne, Switzerland

14 Institute of Biochemistry and Molecular Medicine, University of Bern, Buehlstrasse 28, 3000, Bern 9, Switzerland

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BMC Genomics 2012, 13:274  doi:10.1186/1471-2164-13-274

Published: 22 June 2012

Additional files

Additional file 1:

Table S2.Gene sets used for data analysis

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Additional file 2:

Figure S1. Solute carriers of plasma membrane profiles of small intestinal enterocytes most similar to Caco-2 cells. Heatmap of relative expression levels of solute carriers of the plasma membrane.

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Additional file 3:

Figure S2. Differentiated Caco-2, HT29 and T84 cell lines most similar to enterocytes with respect to expression ABC transporters. Heatmap of the relative expression levels of ABC transporters.

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Additional file 4:

Figure S3. Two distinct groups of genes with respect to expected chemosensitivity. Heatmap of correlation coefficients –log(GI50) of 50 chemotherapeutics and expression values across the NCI60 cell line panel.

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Additional file 5:

Table 1S. List of expression files used for microarray analysis and corresponding accession numbers at Gene Expression Omnibus.

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Additional file 6:

Supplementary information for methods and additional results[29,30,41,55-58]

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Additional file 7:

Figure S4. Enrichment of small intestinal signature in Caco-2 cells upon differentiation. Heatmap representing enrichment scores obtained by gene set enrichment analysis of the selected panel of gene sets. Genes in the various cell lines were ranked according to their relative average expression (n = 2-3) in the given cell line compared to a panel of healthy epithelial tissues. Details see Additional file 6, material and methods.

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