This method was initially used for data exploration to determine the gene expre

Genes were manually selected on the basis of meeting two or more of these criteria and as representatives to validate the typically less quantitative array data analyses. These 19 Amuvatinib 850879-09-3 genes are listed in Table 3 along with the TFs that are predicted to target them. The predicted targets of the majority of the TFs identified by CIA are statistically overrepresented in the 421 genes associated with the response to lapatinib In order to validate the results obtained by CIA we used a fisher exact test to determine if the predicted targets of the 8 TFs identified, were enriched in the 421 genes associated with the response to lapatinib. The results are shown in Additional file 4. The 8 TFs are represented by 6 motifs. Of these 6 motifs, 4 are significantly overrepre sented in the promoters of the 421 lapatinib responsive genes, while two are not.<br><br> While none of these transcription factors are present in the 421 gene list their predicted targets are modulated buy AT-406 in response to lapatinib for the majority of the TFs identified. Lapatinib toxicological analysis in a panel of cell lines using acid phosphatase proliferation assay identifies a range of drug responses in breast cancer The IC50 values determined using the described methods were found to correlate with previous published data for 5 of the 6 cell lines. There are currently no publically available IC50 values for lapatinib response in MDAMB231 cells. The values determined were 0. 036 0. 0151 um for BT474, 0. 080 0. 0173 uM for SKBR3, 0. 193 0. 0665 uM for EFM192A, 0. 4166 0. 18 uM for HCC1954, 6. 08 0. 825 uM for MDAMB453 and 7.<br><br> 46 0. 102 uM for MDAMB231. Taqman PCR analysis confirms dysregulation of the 8 transcription factors following lapatinib exposure The initial Taqman RT PCR analysis was carried out in lapatinib treated BT474 and SKBR3 breast cancer cell lines. AG-490 133550-30-8 The drug concentration and treatment duration were also evaluated using the CIA. The combination of 1 uM lapatinib and 12 hours post treatment are the opti mal conditions for treating the cells based on the separa tions seen in Figures 1 and 2. In addition, 1 uM of lapatinib is a clinically relevant concentration. These two cell lines are highly sensitive to lapatinib with IC50 values of 0. 036 uM 0. 0151 uM and 0. 080 uM 0. 0173 uM respectively. Four additional cell lines were also chosen based on their sensi tivity to lapatinib.<br><br> Their IC50 values are shown in Table 4. 76 of the 8 transcription factors were found to be present following 1 uM 12 hr lapatinib treatment relative to untreated controls. Although these genes were not identified from the differential gene expression analysis, they are clearly dysregulated in these cell lines, as predicted by CIA. 2 of the predicted transcription factors were not expressed. While the expression of the transcription factors does not follow a set pattern, there are some distinct trends. For ex ample, all the TFs were up regulated in the most lapatinib sensitive cell line and nearly all down regulated in the most lapatinib insensitive cell line. In addition ARNT was up regulated in all lines, apart from MDAMB231, the triple negative cell line.