- WBPaper00040876:mir-35_upregulated
The raw data was normalized and t-statics were computed using R and Bioconductor with the affy package and Benjamini-Hoch-berg (BH) correction method for multiple comparisons. RNA levels that changed at least 1.5-fold with a probability of p < 0.005 after BH correction were considered significantly different in mir-35(gk262) mutants relative to wild-type.
Genes with expression level up regulated in mir-35 mutants comparing with N2.
- WBPaper00040876:mir-35_downregulated
The raw data was normalized and t-statics were computed using R and Bioconductor with the affy package and Benjamini-Hoch-berg (BH) correction method for multiple comparisons. RNA levels that changed at least 1.5-fold with a probability of p < 0.005 after BH correction were considered significantly different in mir-35(gk262) mutants relative to wild-type.
Genes with expression level down regulated in mir-35 mutants comparing with N2.
- WBPaper00031850:mdt-15(RNAi)_upregulated
Author used empirical Bayes fitting in limma with multiple hypothesis correction method BH, and considered genes with a P-value < 0.05 to be differentially expressed.
Genes upregulated in mdt-15(RNAi) animals comparing with control.
- WBPaper00031850:mdt-15(RNAi)_downregulated
Author used empirical Bayes fitting in limma with multiple hypothesis correction method BH, and considered genes with a P-value < 0.05 to be differentially expressed.
Genes downregulated in mdt-15(RNAi) animals comparing with control.
- WBPaper00060479:sid-2(mj465)_upregulated
FDR < 0.01, fold change > 2. Stistical analysis was performed using Benjamini-Hochberg (BH) adjustment using the MATLAB (Mathworks) function nbintest with the VarianceLink setting LocalRegression.
Transcripts that showed significantly increased expression in sid-2(mj465) animals comparing to in N2.
- WBPaper00060479:sid-2(mj465)_downregulated
FDR < 0.01, fold change > 2. Stistical analysis was performed using Benjamini-Hochberg (BH) adjustment using the MATLAB (Mathworks) function nbintest with the VarianceLink setting LocalRegression.
Transcripts that showed significantly decreased expression in sid-2(mj465) animals comparing to in N2.
- WBPaper00042274:tbx-2(bx59)_upregulated
The limma package was used to calculate differential expression using the limma linear model fit, eBayes smoothing of standard errors, and Benjamini-hochberg(Bh) multiple test correction with a false discovery rate of 5%.
Genes with increased expression in tbx-2(bx59) comparing to N2.
- WBPaper00042274:tbx-2(bx59)_downregulated
The limma package was used to calculate differential expression using the limma linear model fit, eBayes smoothing of standard errors, and Benjamini-hochberg(Bh) multiple test correction with a false discovery rate of 5%.
Genes with decreased expression in tbx-2(bx59) comparing to N2.
- WBPaper00062305:P.brevicompactum_upregulated
voom from limma v 3.42.2 was applied to estimate fold changes and BH-adjusted p-values.
Transcripts that showed significantly increased expression after L1 stage N2 animals were grown on plates covered by mold Penicillium brevicompacum with E. coli OP50 for 48 hours at 20 centigrade.
- WBPaper00062305:P.brevicompactum_downregulated
voom from limma v 3.42.2 was applied to estimate fold changes and BH-adjusted p-values.
Transcripts that showed significantly decreased expression after L1 stage N2 animals were grown on plates covered by mold Penicillium brevicompacum with E. coli OP50 for 48 hours at 20 centigrade.