WormBase Tree Display for Expression_cluster: WBPaper00037113:CPF_16C_up-regulated
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| WBPaper00037113:CPF_16C_up-regulated | Description | Up-regulated genes under 0.5mg/l CPF treatment at 16 centigrade. | |
|---|---|---|---|
| Species | Caenorhabditis elegans | ||
| Algorithm | The Rank Product package was used to identify the differentially expressed genes between controls and treatment in each experiment. Briefly, genes were ranked based on up- or downregulation by the treatment in each experiment. Then, for each gene a combined probability was calculated as a rank product (RP). The RP values were used to rank the genes based on how likely it was to observe them by chance at that particular position on the list of differentially expressed genes. The RP can be interpreted as a p-value. To determine significance levels, the RP method uses a permutation-based estimation procedure to transform the p-value into an e-value that addresses the multiple testing problem derived from testing many genes simultaneously. Genes with a percentage of false-positives (PFP) < 0.05 were considered differentially expressed between treatments and control in each experiment. This method has the advantage to identify genes with a response to the toxicants even when the absolute effect of the response was low. Because authors used sub-lethal concentrations of the toxicants, methods that use thresholds based on absolute fold change would not identify small changes in gene expression. Moreover, RP has proved to be a robust method for comparing microarray data from different sources and experiments. | ||
| Reference | WBPaper00037113 | ||
| Microarray_results (177) | |||
| Gene (162) | |||
| Attribute_of | Microarray_experiment | WBPaper00037113:Control_vs_CPF-(0.5)_Rep1 | |
| WBPaper00037113:Control_vs_CPF-(0.5)_Rep2 | |||
| WBPaper00037113:Control_vs_CPF-(0.5)_Rep3 | |||
| WBPaper00037113:CPF-(0.5)_vs_Control_Rep1 | |||
| WBPaper00037113:CPF-(0.5)_vs_Control_Rep2 | |||
| WBPaper00037113:CPF-(0.5)_vs_Control_Rep3 | |||
| Regulation | Regulated_by_molecule | WBMol:00003591 | |
| Associated_with | Life_stage | WBls:0000038 |
