PMC:7572125 / 32144-35293 JSONTXT

{"project":"2_test","denotations":[{"id":"33073769-22000013-27525633","span":{"begin":2727,"end":2731},"obj":"22000013"}],"text":"For wild-type HCT116 cells, we found that compared to cells transfected with control siRNA, depletion of VAPA, CNOT6L, or PTEN resulted in different levels of increased cell proliferation (Figure 4, Figure 4—figure supplement 1A). For DicerEx5 HCT116 cells, depletion of PTEN resulted in increased cell proliferation compared to control siRNA with a similar magnitude as wild-type cells, depletion of VAPA resulted in an increased proliferation compared to control siRNA, but not at the same magnitude as occurred in wild-type cells, while depletion of CNOT6L resulted in a slight decrease in cell proliferation compared to control siRNA. To test if depletion of the putative PTEN ceRNAs increased proliferation in wild-type HCT116 cells and were attenuated in the DicerEx5 HCT116 cells, we performed an analysis of variance (ANOVA) on the AUC for each biological repeat. The ANOVA result was statistically significant for the siRNA main effect (F(3,24) = 12.1, p=5.20×10−5). Thus, the null hypothesis that there is no difference in cell proliferation when the putative PTEN ceRNAs or PTEN was depleted, whether or not it was conducted in wild-type or DicerEx5 HCT116 cells, can be rejected. The main effect for cell type (F(1,24) = 1.81, p=0.191) was not statistically significant, indicating the null hypothesis that there is no difference in cell proliferation between wild-type or DicerEx5 HCT116 cells can not be rejected, and the interaction effect was not statistically significant (F(3,24) = 0.734, p=0.542). These results suggest that while there were differences in cell proliferation when the putative PTEN ceRNAs or PTEN were depleted, it was similar between cell lines suggesting a lack of an attenuated ceRNA effect. We also conducted six comparisons using the Bonferroni correction to adjust for multiple comparisons, making the a priori adjusted significance threshold 0.0083. According to this criterion, depletion of PTEN in wild-type or DicerEx5 HCT116 cells resulted in statistically significant increases in cell proliferation compared to control siRNA. Depletion of VAPA or CNOT6L did not result in a statistically significant increase in cell proliferation compared to control siRNA in wild-type HCT116 cells. Additionally, depletion of CNOT6L, but not VAPA, resulted in a statistically significant decrease in cell proliferation compared to PTEN-depleted DicerEx5 HCT116 cells. The original study reported reduced expression of VAPA or CNOT6L in wild-type HCT116 cells resulted in a statistically significant increase in cell proliferation compared to control siRNA similar to what was observed with PTEN siRNA, which was statistically significantly attenuated in the DicerEx5 HCT116 cells (Tay et al., 2011). Further, the original study (DicerEx5: 1–15%; wild-type: 5–10%) and this replication attempt (DicerEx5: 6–19%; wild-type: 5–10%) observed similar RSDs. To summarize, for this experiment we found results that varied in statistical significance and varied in direction relative to the original study for the putative PTEN ceRNAs, but were in the same direction as the original study for cells transfected with siPTEN."}

{"project":"MyTest","denotations":[{"id":"33073769-22000013-27525633","span":{"begin":2727,"end":2731},"obj":"22000013"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"For wild-type HCT116 cells, we found that compared to cells transfected with control siRNA, depletion of VAPA, CNOT6L, or PTEN resulted in different levels of increased cell proliferation (Figure 4, Figure 4—figure supplement 1A). For DicerEx5 HCT116 cells, depletion of PTEN resulted in increased cell proliferation compared to control siRNA with a similar magnitude as wild-type cells, depletion of VAPA resulted in an increased proliferation compared to control siRNA, but not at the same magnitude as occurred in wild-type cells, while depletion of CNOT6L resulted in a slight decrease in cell proliferation compared to control siRNA. To test if depletion of the putative PTEN ceRNAs increased proliferation in wild-type HCT116 cells and were attenuated in the DicerEx5 HCT116 cells, we performed an analysis of variance (ANOVA) on the AUC for each biological repeat. The ANOVA result was statistically significant for the siRNA main effect (F(3,24) = 12.1, p=5.20×10−5). Thus, the null hypothesis that there is no difference in cell proliferation when the putative PTEN ceRNAs or PTEN was depleted, whether or not it was conducted in wild-type or DicerEx5 HCT116 cells, can be rejected. The main effect for cell type (F(1,24) = 1.81, p=0.191) was not statistically significant, indicating the null hypothesis that there is no difference in cell proliferation between wild-type or DicerEx5 HCT116 cells can not be rejected, and the interaction effect was not statistically significant (F(3,24) = 0.734, p=0.542). These results suggest that while there were differences in cell proliferation when the putative PTEN ceRNAs or PTEN were depleted, it was similar between cell lines suggesting a lack of an attenuated ceRNA effect. We also conducted six comparisons using the Bonferroni correction to adjust for multiple comparisons, making the a priori adjusted significance threshold 0.0083. According to this criterion, depletion of PTEN in wild-type or DicerEx5 HCT116 cells resulted in statistically significant increases in cell proliferation compared to control siRNA. Depletion of VAPA or CNOT6L did not result in a statistically significant increase in cell proliferation compared to control siRNA in wild-type HCT116 cells. Additionally, depletion of CNOT6L, but not VAPA, resulted in a statistically significant decrease in cell proliferation compared to PTEN-depleted DicerEx5 HCT116 cells. The original study reported reduced expression of VAPA or CNOT6L in wild-type HCT116 cells resulted in a statistically significant increase in cell proliferation compared to control siRNA similar to what was observed with PTEN siRNA, which was statistically significantly attenuated in the DicerEx5 HCT116 cells (Tay et al., 2011). Further, the original study (DicerEx5: 1–15%; wild-type: 5–10%) and this replication attempt (DicerEx5: 6–19%; wild-type: 5–10%) observed similar RSDs. To summarize, for this experiment we found results that varied in statistical significance and varied in direction relative to the original study for the putative PTEN ceRNAs, but were in the same direction as the original study for cells transfected with siPTEN."}