Genome-wide expression patterns of invasion front, inner tumor mass and surrounding normal epithelium of colorectal tumors

doi:10.1186/1476-4598-6-79

Molecular Cancer

Volume 6

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Staub E
Groene J
Heinze M
Mennerich D
Roepcke S
Klaman I
Hinzmann B
Castanos-Velez E
Pilarsky C
Mann B
Brümmendorf T
Weber B
Buhr HJ
Rosenthal A

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Staub E
Groene J
Heinze M
Mennerich D
Roepcke S
Klaman I
Hinzmann B
Castanos-Velez E
Pilarsky C
Mann B
Brümmendorf T
Weber B
Buhr HJ
Rosenthal A
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Genome-wide expression patterns of invasion front, inner tumor mass and surrounding normal epithelium of colorectal tumors

Eike Staub¹^,2 , Joern Groene⁴ , Maya Heinze⁴ , Detlev Mennerich⁵ , Stefan Roepcke¹^,11 , Irina Klaman⁶ , Bernd Hinzmann⁶ , Esmeralda Castanos-Velez⁷ , Christian Pilarsky⁸ , Benno Mann⁹ , Thomas Brümmendorf³^,10 , Birgit Weber³^,12 , Heinz-Johannes Buhr⁴ and André Rosenthal⁶

¹Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany

²Merck Serono, Bio- & Chemoinformatics, Darmstadt, Germany

³metaGen Pharmaceuticals i.L., Berlin, Germany

⁴Charité – Campus Benjamin Franklin, Department of General, Vascular and Thoracic Surgery, Berlin, Germany

⁵Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany

⁶Signature Diagnostics, Potsdam, Germany

⁷Epigenomics, Berlin, Germany

⁸University Hospital Carl Gustav Carus Dresden, Department of Visceral, Thoracic, and Vascular Surgery, Germany

⁹Augusta-Kranken-Anstalt GmbH, Department of Surgery, Bochum, Germany

¹⁰Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland

¹¹Nycomed, Konstanz, Germany

¹²ratiopharm, Ulm, Germany

author email corresponding author email

Molecular Cancer 2007, 6:79doi:10.1186/1476-4598-6-79


Published:	14 December 2007

Additional files

Additional File 1:

Microarray expression data of 7433 genes. The pre-processed expression data for all 7433 genes that were considered for subsequent analysis. The data are logarithms (base e) of expression ratios between each measurement and the mean value over all experiments with normal epithelia. Therefore, these log ratios indicate relative changes compared to normal epithelia. Positive values indicate up-regulation compared to normal epithelia. For further preprocessing steps see legend of Figure 1 in the manuscript.

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Additional File 2:

Results from statistical tests for differential expression. These tables comprise results from statistical testing for differential gene expression and the annotations for all 7433 genes. The gene-wise p-values and Q-values of unpaired Welch test or the paired t-test (Benjamini-Hochberg method) for each sample group comparison are listed. The gene group memberships of each gene are separated by a colon in the respective column. KEGG, GenMAPP and GO categories for all genes were taken from the Affymetrix U133A DNA chip annotation http://netaffx.com webcite. All other gene groups were taken from the MSIGDB database http://www.broad.mit.edu/gsea/msigdb/msigdb_index.html webcite.

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Additional File 3:

Significantly deregulated gene groups. Here we show the results of Fisher's Exact test for the over-representation of functional gene groups among up- or down-regulated genes in colorectal tumors of our study. To correct for multiple testing Q-values were calculated using the Benjamini-Hochberg method.

Format: XLS Size: 39KB Download file

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