- WBPaper00036286:Pattern_H
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.
Expression Pattern Group H, enriched for genes involved in embryonic development. These patterns have in common that they all have genes of which the expression goes up after the juvenile stage. The expression of the genes in these patterns remains high or even goes up after reproduction.
- WBPaper00026952:class_H
Raw data from each experiment were downloaded from the Stanford Microarray Database into Excel files and processed as follows: (i) sort by Spot Flag and discard any rows where the Spot Flag value was nonzero, indicating a bad PCR; (ii) sort by Failed and discard any rows where the Failed value was nonzero, indicating abnormal hybridization; (iii) import into a common file for each type of experiment (i.e., lin-14 or lin-4) the columns from each raw experimental file [RAT2(R/G), which shows a log base 2 transformed ratio of normalized red/green signal for each spot; name of spot (Wormbase designation); chromosome location and description (www.wormbase.org)]; (iv) calculate an average RAT2(R/G) based on the 2 or 3 values (avg; any rows which had only one good experimental value were discarded); (v) calculate a standard deviation (stdev) for the average value; (vi) calculate a t value for each spot by using the formula t = avg*[sqrt(n - 1)]/stdev, where n is the number of experiments for which good data exist, sqrt is square root, and stdev is standard deviation; (vii) sort by absolute t value and discard any rows with a t value below 4.303 (below 95% confidence interval for three experiments) or below 12.706 (below 95% confidence interval for two experiments); (viii) sort by absolute average value and discard any rows with average values below 1.0 (less than twofold change compared to control).
Class H gene expression showed up regulation in lin-14(lf) in L1, up regulation in lin-4(lf) in L2.
- WBPaper00034636:heat_shock_upregulated
paired t-tests
Genes Showing Significant Expression Changes (P <= 0.05 After FDR) in Heat-Shocked (30 centigrade for 1.5 h; Two Arrays), Compared to Sham Controls (26 centigrade for 2.5 h; Five Arrays).
- WBPaper00034636:heat_shock_downregulated
paired t-tests
Genes Showing Significant Expression Changes (P <= 0.05 After FDR) in Heat-Shocked (30 centigrade for 1.5 h; Two Arrays), Compared to Sham Controls (26 centigrade for 2.5 h; Five Arrays).
- WBPaper00065225:nhr-42(tm1375)_upregulated_S.aureus-infected
Adjusted p-value (Padj) <= 0.01 was considered significant for differential gene expression.
Transcripts that showed significantly increased expression in nhr-42(tm1375) animals infected with S. aureus SH1000 for 5 h, comparing to in N2 animals infected with S. aureus SH1000 for 5 h.
- WBPaper00065225:nhr-42(tm1375)_downregulated_S.aureus-infected
Adjusted p-value (Padj) <= 0.01 was considered significant for differential gene expression.
Transcripts that showed significantly decreased expression in nhr-42(tm1375) animals infected with S. aureus SH1000 for 5 h, comparing to in N2 animals infected with S. aureus SH1000 for 5 h.