WBPaper00041097:pgl-1_upregulated

The threshold for the detected proteins and matched peptides was set at sequence coverage >= 20% and ProteinPilot unused score >= 1.31 (a confidence threshold of 95%). Theoretical pI and Mw of each identified protein were calculated by using the pI/Mw tool of the ExPASy proteomic server (Swiss Institute of Bioinformatics, Lausanne, Switzerland). Proteins constantly downregulated in pgl-1(bn101) and pgl-1(ct131) at both 20 C and 25 C, according to 2D-DIGE and LC-MS/MS.

WBPaper00041097:pgl-1_downregulated

The threshold for the detected proteins and matched peptides was set at sequence coverage >= 20% and ProteinPilot unused score >= 1.31 (a confidence threshold of 95%). Theoretical pI and Mw of each identified protein were calculated by using the pI/Mw tool of the ExPASy proteomic server (Swiss Institute of Bioinformatics, Lausanne, Switzerland). Proteins constantly downregulated in pgl-1(bn101) and pgl-1(ct131) at both 20 C and 25 C, according to 2D-DIGE and LC-MS/MS.

[cgc5767]:expression_class_E_pi(83_min)

A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. Embryonic (E) subclasses are based on the earliest significant increase(abbreviated pi for primary increase).

[cgc5767]:expression_class_SE_pi(66_min)

A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. Strictly embryonic (SE) subclasses are based on the earliest significant increase(abbreviated pi for primary increase).

[cgc5767]:expression_class_E_pi(23_min)

A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. Embryonic (E) subclasses are based on the earliest significant increase(abbreviated pi for primary increase).

[cgc5767]:expression_class_SE_pi(41_min)

A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. Strictly embryonic (SE) subclasses are based on the earliest significant increase(abbreviated pi for primary increase).

[cgc5767]:expression_class_SE_pi(53_min)

A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. Strictly embryonic (SE) subclasses are based on the earliest significant increase(abbreviated pi for primary increase).

[cgc5767]:expression_class_SE_pi(122_min)

A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. Strictly embryonic (SE) subclasses are based on the earliest significant increase(abbreviated pi for primary increase).

[cgc5767]:expression_class_SE_pi(186_min)

A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. Strictly embryonic (SE) subclasses are based on the earliest significant increase(abbreviated pi for primary increase).

[cgc5767]:expression_class_SE_pi(PC32)

A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. Strictly embryonic (SE) subclasses are based on the earliest significant increase(abbreviated pi for primary increase).