- WBPaper00044452:ace_1_ace-2_downregulated
Proteins that showed more than 4 fold change in expression are considered differentially expressed.
Proteins that showed decreased expression for more than 4 fold in ace-1(p1000);ace-2(g72) comparing to in N2, according to 2DE LS-MS/MS analysis.
- WBPaper00044452:ace_1_ace-2_upregulated
Proteins that showed more than 4 fold change in expression are considered differentially expressed.
Proteins that showed increased expression for more than 4 fold in ace-1(p1000);ace-2(g72) comparing to in N2, according to 2DE LS-MS/MS analysis.
- WBPaper00046497:B.thuringiensis_upregulated_protein
Quantitative results of log2 transformed iTRAQ-protein ratios describing the condition pathogenic/non-pathogenic BT were tested against all log2 transformed control-ratios of biological replicates in the same iTRAQ experiment using the two sided Welchs t-test. To adjust for multiple testing, p-values were corrected by permutation based FDR approach with 1000 randomizations. Protein groups with log2 ratios of at least +/- 0.485 (which corresponds to iTRAQ-ratios >= 1.4 or <= 0.71) with FDR-corrected p-value <= 0.05 were considered to be differentially expressed.
Proteins that showed significantly increased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT, according to proteomic studies via isobaric labelling and 2D-LS-MS/MS.
- WBPaper00046497:B.thuringiensis_downregulated_protein
Quantitative results of log2 transformed iTRAQ-protein ratios describing the condition pathogenic/non-pathogenic BT were tested against all log2 transformed control-ratios of biological replicates in the same iTRAQ experiment using the two sided Welchs t-test. To adjust for multiple testing, p-values were corrected by permutation based FDR approach with 1000 randomizations. Protein groups with log2 ratios of at least +/- 0.485 (which corresponds to iTRAQ-ratios >= 1.4 or <= 0.71) with FDR-corrected p-value <= 0.05 were considered to be differentially expressed.
Proteins that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT, according to proteomic studies via isobaric labelling and 2D-LS-MS/MS.
- WBPaper00041002:HQ_3d_0.2mM_Down
For selection of DEGs, an unpaired t -test was performed followed by a significance analysis of microarray (SAM) test including a calculation that estimates the false discovery rate (FDR). FDR, reducing on the one hand type I errors for null associations, was set to a non-stringent level of <12.5%, mainly to guard from an increase of type II error and also based on findings by Levine et al. (2011), which described 12.5% as most acceptable optimum level of FDR, representing the 90th percentile of the normal distribution curve. DEGs exceeding a fold change of 1.25 were further analyzed with respect to their functional clustering. This fold-cut-off was chosen to allow an interpretation that is biologically meaningful, akin to the notion that data of sound technical and experimental quality which returns strong, statistically significant, absolute signal intensities is sufficiently robust to justify a fold-cut-off of >1.2. This analysis was conducted using the functional annotation clustering tool of the Database for Annotation, Visualization, and Integrated Discovery (DAVID; Huang et al., 2007).
Gene significantly down-regulated by treatment with 0.2mM of HuminFeed Hydroquinone until young adult stage (3 days), with a minimum fold change in gene expression of 0.8.
- WBPaper00041002:HF_3d_2.0mM_Down
For selection of DEGs, an unpaired t -test was performed followed by a significance analysis of microarray (SAM) test including a calculation that estimates the false discovery rate (FDR). FDR, reducing on the one hand type I errors for null associations, was set to a non-stringent level of <12.5%, mainly to guard from an increase of type II error and also based on findings by Levine et al. (2011), which described 12.5% as most acceptable optimum level of FDR, representing the 90th percentile of the normal distribution curve. DEGs exceeding a fold change of 1.25 were further analyzed with respect to their functional clustering. This fold-cut-off was chosen to allow an interpretation that is biologically meaningful, akin to the notion that data of sound technical and experimental quality which returns strong, statistically significant, absolute signal intensities is sufficiently robust to justify a fold-cut-off of >1.2. This analysis was conducted using the functional annotation clustering tool of the Database for Annotation, Visualization, and Integrated Discovery (DAVID; Huang et al., 2007).
Gene significantly down-regulated by treatment with 2.0mM of HuminFeed until young adult stage (3 days), with a minimum fold change in gene expression of 0.8.
- WBPaper00041002:HF_3d_0.2mM_Down
For selection of DEGs, an unpaired t -test was performed followed by a significance analysis of microarray (SAM) test including a calculation that estimates the false discovery rate (FDR). FDR, reducing on the one hand type I errors for null associations, was set to a non-stringent level of <12.5%, mainly to guard from an increase of type II error and also based on findings by Levine et al. (2011), which described 12.5% as most acceptable optimum level of FDR, representing the 90th percentile of the normal distribution curve. DEGs exceeding a fold change of 1.25 were further analyzed with respect to their functional clustering. This fold-cut-off was chosen to allow an interpretation that is biologically meaningful, akin to the notion that data of sound technical and experimental quality which returns strong, statistically significant, absolute signal intensities is sufficiently robust to justify a fold-cut-off of >1.2. This analysis was conducted using the functional annotation clustering tool of the Database for Annotation, Visualization, and Integrated Discovery (DAVID; Huang et al., 2007).
Gene significantly down-regulated by treatment with 0.2mM of HuminFeed until young adult stage (3 days), with a minimum fold change in gene expression of 0.8.
- WBPaper00041002:HF_11d_0.2mM_Up
For selection of DEGs, an unpaired t -test was performed followed by a significance analysis of microarray (SAM) test including a calculation that estimates the false discovery rate (FDR). FDR, reducing on the one hand type I errors for null associations, was set to a non-stringent level of <12.5%, mainly to guard from an increase of type II error and also based on findings by Levine et al. (2011), which described 12.5% as most acceptable optimum level of FDR, representing the 90th percentile of the normal distribution curve. DEGs exceeding a fold change of 1.25 were further analyzed with respect to their functional clustering. This fold-cut-off was chosen to allow an interpretation that is biologically meaningful, akin to the notion that data of sound technical and experimental quality which returns strong, statistically significant, absolute signal intensities is sufficiently robust to justify a fold-cut-off of >1.2. This analysis was conducted using the functional annotation clustering tool of the Database for Annotation, Visualization, and Integrated Discovery (DAVID; Huang et al., 2007).
Gene significantly up-regulated by treatment with 0.2mM of HuminFeed until older adult stage (11 days), with a minimum fold change in gene expression of 1.25.
- WBPaper00041002:HF_11d_2.0mM_Down
For selection of DEGs, an unpaired t -test was performed followed by a significance analysis of microarray (SAM) test including a calculation that estimates the false discovery rate (FDR). FDR, reducing on the one hand type I errors for null associations, was set to a non-stringent level of <12.5%, mainly to guard from an increase of type II error and also based on findings by Levine et al. (2011), which described 12.5% as most acceptable optimum level of FDR, representing the 90th percentile of the normal distribution curve. DEGs exceeding a fold change of 1.25 were further analyzed with respect to their functional clustering. This fold-cut-off was chosen to allow an interpretation that is biologically meaningful, akin to the notion that data of sound technical and experimental quality which returns strong, statistically significant, absolute signal intensities is sufficiently robust to justify a fold-cut-off of >1.2. This analysis was conducted using the functional annotation clustering tool of the Database for Annotation, Visualization, and Integrated Discovery (DAVID; Huang et al., 2007).
Gene significantly down-regulated by treatment with 2.0mM of HuminFeed until older adult stage (11 days), with a minimum fold change in gene expression of 0.8.
- WBPaper00041002:HQ_3d_0.2mM_Up
For selection of DEGs, an unpaired t -test was performed followed by a significance analysis of microarray (SAM) test including a calculation that estimates the false discovery rate (FDR). FDR, reducing on the one hand type I errors for null associations, was set to a non-stringent level of <12.5%, mainly to guard from an increase of type II error and also based on findings by Levine et al. (2011), which described 12.5% as most acceptable optimum level of FDR, representing the 90th percentile of the normal distribution curve. DEGs exceeding a fold change of 1.25 were further analyzed with respect to their functional clustering. This fold-cut-off was chosen to allow an interpretation that is biologically meaningful, akin to the notion that data of sound technical and experimental quality which returns strong, statistically significant, absolute signal intensities is sufficiently robust to justify a fold-cut-off of >1.2. This analysis was conducted using the functional annotation clustering tool of the Database for Annotation, Visualization, and Integrated Discovery (DAVID; Huang et al., 2007).
Gene significantly up-regulated by treatment with 0.2mM of HuminFeed Hydroquinone until young adult stage (3 days), with a minimum fold change in gene expression of 1.25.