WBPaper00059824:rnp-6(dh1127)_regulated_OP50

Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2. Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with heat killed E. coli OP50.

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.

WBPaper00049990:glp-4(bn2)_26C_vs_15C_upregulated

DESeq2 q-value < 0.05. miRNAs that showed significantly increased expression in glp-4(bn2) at 26 centigrade than in 15 centigrade.

WBPaper00064107:lin-35(n745)_downregulated

DESeq2, Fold < -1.5 or > 1.5, q <0.05 Transcripts that showed significantly decreased expression in lin-35(n745) comparing to in N2.

WBPaper00049990:glp-4(bn2)_26C_vs_15C_downregulated

DESeq2 q-value < 0.05. miRNAs that showed significantly decreased expression in glp-4(bn2) at 26 centigrade than in 15 centigrade.