WBPaper00038168:lin-35_upregulated

For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis. Genes that were upregulated in lin-35.

WBPaper00038168:lin-35_downregulated

For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis. Genes that were downregulated in lin-35.

WBPaper00038168:lin-15B(n744)_downregulated

For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis. Genes that were downregulated in lin-15B(n744).

WBPaper00038168:lin-15B(n744)_upregulated

For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis. Genes that were upregulated in lin-15B(n744).

WBPaper00052881:B.subtilis-biofilm_upregulated

CuffDiff q-value < 0.05. Transcripts that showed significantly increased expression after the formation of B. subtilis biofilm

WBPaper00052881:B.subtilis-biofilm_downregulated

CuffDiff q-value < 0.05. Transcripts that showed significantly decreased expression after the formation of B. subtilis biofilm

WBPaper00064565:dyf-1(mn335)_regulated_protein

FDR < 0.1 Significantly affected proteins in dyf-1(mn335) compared with wild-type (q-value cut off 0.1)

WBPaper00042477:RSR-2_complex

Percolator (semi-supervised learning machine) was used at constant 0.01% FDR. Percolator assigns a q-value to each spectrum, which is defined as the minimal FDR at which the identification is deemed correct. These q values are estimated using the distribution of scores from decoy database search, and the q-value threshold was set to <0.01 to validate any peptide. Proteins contained in RSR-2 complex, according to immunoprecipitation using anti-RSR-2, and MudPIT, liquid chromatography and mass spectrometry.

WBPaper00051388:Glucose-diet_upregulated

CuffDiff, q-value < 0.05 Transcripts that showed significantly increased expression in NGM+Glucose diet for 20h at 20C, comparing to in NGM.

WBPaper00058925:acox-1.1(ok2257)_downregulated

DESeq2, q-value < 0.01 Transcripts that showed significantly decreased expression in acox-1.1(ok2257) comparing to in N2 at L4 larva stage.