GW637

Caenorhabditis elegans

WBPaper00058942:henn-1(pk2295)_upregulated

Differential expression analysis, including fold change and p value calculation, was done using DESeq2 v.1.18.1 with the Benjamin Hochberg multiple test correction applied (FDR = 0.05). mRNAs significantly upregulated >1.3 fold in henn-1(pk2295) gonads comparing to in N2 gonads 68 - 70 hours after L1 larva stage.

WBPaper00058942:henn-1(pk2295)_downregulated

Differential expression analysis, including fold change and p value calculation, was done using DESeq2 v.1.18.1 with the Benjamin Hochberg multiple test correction applied (FDR = 0.05). mRNAs significantly downregulated >1.3 fold in henn-1(pk2295) gonads comparing to in N2 gonads 68 - 70 hours after L1 larva stage.

WBPaper00038172:tax-6null_down_regulated

To identify genes that were significantly differentially expressed between each mutant and the control, linear modelling and empirical Bayes analysis was performed using the limma package. Limma computes an empirical Bayes adjustment for the t-test (moderated t-statistic), which is more robust than the standard two-sample t-test comparisons. To correct for multiple testing, Benjamin and Hochbergs method to control for false discovery rate was used. Genes with an adjusted P value of 0.05 or smaller and a fold-change in expression larger than twofold were considered differentially expressed. Genes down regulated in tax-6(ok2065) comparing to in N2.

WBPaper00038172:crh-1null_down_regulated

To identify genes that were significantly differentially expressed between each mutant and the control, linear modelling and empirical Bayes analysis was performed using the limma package. Limma computes an empirical Bayes adjustment for the t-test (moderated t-statistic), which is more robust than the standard two-sample t-test comparisons. To correct for multiple testing, Benjamin and Hochbergs method to control for false discovery rate was used. Genes with an adjusted P value of 0.05 or smaller and a fold-change in expression larger than twofold were considered differentially expressed. Genes down regulated in crh-1(nn3315) comparing to in N2.

WBPaper00038172:tax-6null_up_regulated

To identify genes that were significantly differentially expressed between each mutant and the control, linear modelling and empirical Bayes analysis was performed using the limma package. Limma computes an empirical Bayes adjustment for the t-test (moderated t-statistic), which is more robust than the standard two-sample t-test comparisons. To correct for multiple testing, Benjamin and Hochbergs method to control for false discovery rate was used. Genes with an adjusted P value of 0.05 or smaller and a fold-change in expression larger than twofold were considered differentially expressed. Genes up regulated in tax-6(ok2065) comparing to in N2.

WBPaper00038172:aak-2overexpression_up_regulated

To identify genes that were significantly differentially expressed between each mutant and the control, linear modelling and empirical Bayes analysis was performed using the limma package. Limma computes an empirical Bayes adjustment for the t-test (moderated t-statistic), which is more robust than the standard two-sample t-test comparisons. To correct for multiple testing, Benjamin and Hochbergs method to control for false discovery rate was used. Genes with an adjusted P value of 0.05 or smaller and a fold-change in expression larger than twofold were considered differentially expressed. Genes up regulated in aak-2 over expression line uthIs202[Paak-2c

WBPaper00038172:crh-1null_up_regulated

To identify genes that were significantly differentially expressed between each mutant and the control, linear modelling and empirical Bayes analysis was performed using the limma package. Limma computes an empirical Bayes adjustment for the t-test (moderated t-statistic), which is more robust than the standard two-sample t-test comparisons. To correct for multiple testing, Benjamin and Hochbergs method to control for false discovery rate was used. Genes with an adjusted P value of 0.05 or smaller and a fold-change in expression larger than twofold were considered differentially expressed. Genes up regulated in crh-1(nn3315) comparing to in N2.

WBPaper00044638:daf-2(e1370)rsks-1(ok1255)_regulated

A linear model was estimated for each gene to determine if the expression is significantly amplified in the daf-2 rsks-1 double mutant than in the daf-2 and rsks-1 single mutants. An empirical Bayes procedure was performed through the limma package to calculate a moderated t-statistic for each contrast of interest. The p-values were adjusted to control the false discovery rate (FDR) using the Benjamin-Hochberg (BH) procedure. Genes that are differentially expressed in daf-2(e1370) rsks-1(ok1255) to a greater extent than in daf-2 in a DAF-16-dependent manner.

WBPaper00038172:aak-2overexpression_down_regulated

To identify genes that were significantly differentially expressed between each mutant and the control, linear modelling and empirical Bayes analysis was performed using the limma package. Limma computes an empirical Bayes adjustment for the t-test (moderated t-statistic), which is more robust than the standard two-sample t-test comparisons. To correct for multiple testing, Benjamin and Hochbergs method to control for false discovery rate was used. Genes with an adjusted P value of 0.05 or smaller and a fold-change in expression larger than twofold were considered differentially expressed. Genes down regulated in aak-2 over expression line uthIs202 comparing to in N2.