Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways-4

<p><b>Copyright information:</b></p><p>Taken from "Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways"</p><p>http://www.biomedcentral.com/1471-2164/8/117</p><p>BMC Genomics 2007;8():117-117.</p><p>Published online 10 May 2007</p><p>PMCID:PMC1878486.</p><p></p>ey, while the pathways where only one or two cell lines are adequate models are white. The pathway example "RNA Processing" indicates some cell lines were anti-correlated and therefore a quantitative analysis was needed to identify better models that could be used to study this pathway. Error bars were generated from the correlation of a single cell line for each pathway and calculating the standard deviation. The pathways shown here represented a minimum of four cell lines or growth conditions. Numbers in parenthesis indicate how many cell lines were used to calculate the correlation. B: The highest and lowest pathway correlations between normal cervix and cervical cancer. The JNK cascade has a high correlation between normal and tumor, and is modeled well by most cell lines (Figure 5A). Mitosis and a number of other pathways involved in growth and regulation show poor correlation in their gene expression between normal and tumor, as expected. Numbers in parenthesis indicate how many genes were used to calculate the Pearson correlation coefficient

Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways-1

<p><b>Copyright information:</b></p><p>Taken from "Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways"</p><p>http://www.biomedcentral.com/1471-2164/8/117</p><p>BMC Genomics 2007;8():117-117.</p><p>Published online 10 May 2007</p><p>PMCID:PMC1878486.</p><p></p>es, whereas numbered labels represent biological replicates. The primary separation occurs between cell lines (dashed bar) and cervical tissue (solid bar). All GOG samples and CHTN samples #1, 2, 8, 12 and 13 were invasive cervical cancer biopsies. CHTN samples #6, 10, and 11 were normal cervix. Most replicates clustered together, indicating the data was of high quality. Spots present on the microarray that had a median intensity over background of at least 150 and were present in 80% of the arrays were included in the analysis, resulting in 8,338 genes. B: Singular value decomposition of transcriptional profiles reveals general relationships among the samples, positioned here as the projections among the first 3 singular components (accounting for 40% of the variance, [see Additional file ]. Again, cell lines were separated from cervical tissue

Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways-6

<p><b>Copyright information:</b></p><p>Taken from "Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways"</p><p>http://www.biomedcentral.com/1471-2164/8/117</p><p>BMC Genomics 2007;8():117-117.</p><p>Published online 10 May 2007</p><p>PMCID:PMC1878486.</p><p></p>an organotypic environment (white). There were more pathways with a higher correlation to cervical cancer in the organotypic culture than in monolayer (p < 0.004, t-test). Therefore, organotypic cultures were better models of cervical cancer than simple monolayer cultures. B: In the ''Cell-Cell Signaling'' pathway (GO:7267), HeLa cells cultured in an organotypic culture had a higher correlation to both normal cervix and cervical cancer than either monolayer or organotypic control cultures

Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways-2

<p><b>Copyright information:</b></p><p>Taken from "Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways"</p><p>http://www.biomedcentral.com/1471-2164/8/117</p><p>BMC Genomics 2007;8():117-117.</p><p>Published online 10 May 2007</p><p>PMCID:PMC1878486.</p><p></p>vical cancer. Cell lines were cultured in ATCC recommended media as monolayers. SiHa and HeLa cell lines were also cultured in different media as well as in an organotypic environment. In addition to the organotypic culture, a control was used that left out the fibroblasts, which prevented the epithelial cell line to stack in 3-dimensions. The primary, C4-I, and C4-II cell lines had the highest correlation to cervical cancer and therefore were the better general models of cervical cancer out of the cell lines we tested. Changing the media from MEM to DMEM increased the correlation to cervical cancer for the HeLa and SiHa cell lines, as well as culturing them in an organotypic environment. Error bars were derived from the standard deviation of the correlation of a cell line against each individual patient biopsy

Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways-5

<p><b>Copyright information:</b></p><p>Taken from "Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways"</p><p>http://www.biomedcentral.com/1471-2164/8/117</p><p>BMC Genomics 2007;8():117-117.</p><p>Published online 10 May 2007</p><p>PMCID:PMC1878486.</p><p></p> DMEM media versus ATCC recommended MEM media as monolayers. DMEM media contained glucose, and the expression of indicated HeLa cells cultured in DMEM experience a nutrient-rich environment, similar to conditions