WormBase Tree Display for Expression_cluster: WBPaper00044005:DAF-16_upregulated
expand all nodes | collapse all nodes | view schema
| WBPaper00044005:DAF-16_upregulated | Description | Top 50 up regulated genes by DAF-16 based on reanalysis 75 previously published experiments. | |
|---|---|---|---|
| Species | Caenorhabditis elegans | ||
| Algorithm | Authors reanalyzed raw genome-wide expression data from five studies (McElwee et al., 2003; McElwee et al., 2004; Murphy et al., 2003; Shaw et al., 2007; Troemeletal.,2006) encompassing 75 genome-wide expression profiles, which authors used to construct 46 explicit contrasts between conditions with differing levels of DAF-16 activity. After complete reprocessing of the raw data (array-specific standardization, normalization, and remapping of probes), a log-fold-change and corresponding standard error were calculated for each transcript on each array (or array pair for single-channel technologies). Together, these were converted into a vote value between 1 (highly likely to be downregulated) and +1 (highly likely to be upregulated). The total voting score for each gene was computed as the sum of voting scores for individual experiments, which is robust in the sense that the influence of any individual experiment is limited to a single full vote. An empirical null distribution based on random permutation was created, and all genes were ranked from consistently upregulated (class I) to consistently downregulated (class II). The area under the null distribution (p value) for each gene that served as the basis for assigning genes to class I or class II at a 5% false discovery rate. | ||
| Reference | WBPaper00044005 | ||
| Based_on_WB_Release | |||
| Gene (50) | |||
| Attribute_of | Microarray_experiment | ||
| Regulation | Regulated_by_gene | WBGene00000912 | |
| Associated_with | Life_stage | WBls:0000002 |
