WormBase Tree Display for Expression_cluster: WBPaper00036286:Pattern_C

WBPaper00036286:Pattern_C Description: Expression Pattern Group C, enriched for genes involved in metabolic processes.
  Species: Caenorhabditis elegans
  Algorithm: The significance (P 0.0001) of the relative age (time) was used to determine if a gene was differentially expressed between the three age (time) groups. The effect of this factor explaining gene expression differences was used to determine if the expression went up or down during the two age/time periods (t1 - t2 and t2 -t3). Authors used a permutation approach to determine the thresholds for the different mapping strategies. For each of the used models for eQTL mapping, authors used 23,000 permutations. For each permutation, authors randomly picked a spot; each spot could only be picked once. The gene expression and relative lifespan values were than randomly distributed over the RILs (and time points) and used for mapping. In this way, authors obtained a threshold for each of the explaining factors. For the single time points, authors used a FDR of 0.01 to adjust for multiple testing. The genome-wide threshold for this FDR is -log10 P = 3.8 for each of the three time points. For the combined models (t1 to t2 and t2 to t3), authors used a genome-wide threshold of -log10 P = 4, which resembles an FDR of 0.006, 0.001, and 0.006 for marker, age, and the interaction between marker and age, respectively. To determine the threshold for the single gene examples, authors used 1000 permutations as in the genome-wide threshold. The difference is that they use the gene under study in all of the permutations. The P-values for the gene specific thresholds were determined at FDR = 0.05.
  Reference: WBPaper00036286
  Microarray_results (1029)
  Gene (994)
  Attribute_of: Microarray_experiment (54)
  Associated_with: Life_stage: WBls:0000035
      WBls:0000070
      WBls:0000065
    WBProcess: WBbiopr:00000001
  Remark: Type: Co-expression Cluster