Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues

Jan Vydra^*¹ , Irena Selicharová^*² , Kateřina Smutná^*² , Miloslav Šanda^*² , Eva Matoušková^*³^,4^,5 , Eva Buršíková^*³^,4^,5 , Markéta Prchalová^*⁴^,5 , Zuzana Velenská^*⁶ , David Coufal^*⁷ and Jiří Jiráček^*²

¹Department of Oncology, 1st Faculty of Medicine, Charles University Prague, Czech Republic

²Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic

³Institute of Biochemistry and Experimental Oncology, 1st Faculty of Medicine, Charles University Prague, Czech Republic

⁴Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic

⁵Prague Burn Centre, 3rd Faculty of Medicine, Charles University Prague, Czech Republic

⁶Institute of Pathology 1st Faculty of Medicine, Charles University Prague and General Teaching Hospital, Prague, Czech Republic

⁷Institute of Computer Science, Academy of Sciences of the Czech Republic, Prague, Czech Republic

author email corresponding author email* Contributed equally

BMC Cancer 2008, 8:107doi:10.1186/1471-2407-8-107


Published:	16 April 2008

Additional files

Additional file 1:

PDQuest quantity table. The table is in the excel spreadsheet format (PDQuest.xls). Spots are numbered in rows. Means of logarithmic ratios method normalized spot densities in each gel are in columns. The paired gels from each sample (named according to the Table 1) are marked (a) respective (b), for example L40-sp-a, L40-sp-b.

Format: XLS Size: 86KB Download file

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Additional file 2:

Results of the GUHA analysis. The table is in the excel spreadsheet format (guha.xls). Hypotheses are numbered in rows. Antecedent column displays categorized spot intensities. Succedent column displays presence (= 1) or absence (= 0) of metastases at follow-up. Table column displays the contingency table evaluating cedents. Fisher quantifier column corresponds to Fisher's exact test.

Format: XLS Size: 176KB Download file

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Additional file 3:

Results of the R/maanova analysis. The table is in the excel spreadsheet format (maanova.xls). For each spot we show in adequate columns the number given by PDQuest software, log2 difference of log transformed means between metastases and non-metastases groups (fold change), nominal permutation p-values using F1 test statistics (F1 Pvalperm) and false discovery rate adjusted p-values for multiple testing (F1 adjPvalperm). Nominal permutation p-values using Fs test statistics (Fs Pvalperm) and false discovery rate-adjusted p-values for multiple testing (Fs adjPvalperm).

Format: XLS Size: 44KB Download file

This file can be viewed with: Microsoft Excel Viewer