- WBPaper00027339:daf-12(rh273)_upregulated
Differentially expressed genes identified were identified using SAM using delta 0.987 and FDR 5.3.
Genes up-regulated in long-lived daf-12(rh273) are listed including the log2 fold-induction in daf-12(rh273) compared to daf-12(rh61rh411).
- WBPaper00027339:daf-12(rh273)_downregulated
Differentially expressed genes identified were identified using SAM using delta 0.987 and FDR 5.3.
Genes down-regulated in long-lived daf-12(rh273) are listed including the log2 fold-induction in daf-12(rh273) compared to daf-12(rh61rh411).
- WBPaper00040412:germline-regulated_daf-12_target
All lists used an Fs:Ptab 0.01 cutoff.
Genes that were regulated by DAF-12 in response to germline loss, identified by comparing differentially expression genes between glp-1(e2141ts, 25C) vs. glp-1(e2141ts, 20C) and daf-12;glp-1(e2141ts, 25C) vs. daf-12;glp-1(e2141ts, 20C).
- WBPaper00053550:daf-19(m86)_upregulated_L1
BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).
Genes that showed significantly increased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at L1 larva stage.
- WBPaper00053550:daf-19(m86)_downregulated_L1
BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).
Genes that showed significantly decreased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at L1 larva stage.
- WBPaper00053550:daf-19(m86)_downregulated_3-fold-embryo
BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).
Genes that showed significantly decreased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at 3-fold embryo stage.
- WBPaper00053550:daf-19(m86)_downregulated_AdultDay2
BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).
Genes that showed significantly decreased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at 2-day post-L4 adult hermaphrodite stage.
- WBPaper00053550:daf-19(m86)_upregulated_AdultDay2
BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).
Genes that showed significantly increased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at 2-day post-L4 adult hermaphrodite stage.
- WBPaper00053550:daf-19(m86)_upregulated_3-fold-embryo
BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults).
Genes that showed significantly increased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at 3-fold embryo stage.
- WBPaper00040221:DAF-12_target_ALF9
Affymetrix TAS software that computed for each probe estimates of fold enrichment (in linear scale) over hybridization with input DNA. At the same time, TAS calculated for each probe a p-value by applying a Wilcoxon signed rank test. A threshold of 2.5 was selected, which corresponds to probe intensities approximately 2.5 times stronger on the ChIP array than on the Input array. Additional TAS threshold parameters were MinRun=180 bp, MaxGap=300 bp. TAS analysis showed that the selected threshold of 2.5 corresponds approximately to a p-value of 0.01.
Potental DAF-12 target genes identified by ChIP-chip analysis performed on strain ALF9 [daf-12