WBPaper00055060:flr-1(RNAi)_upregulated

N.A. Transcripts that showed significantly increased expression in flr-1(RNAi) comparing to in control RNAi animals. This is an incomplete list.

WBPaper00055060:flr-1(RNAi)_downregulated

N.A. Transcripts that showed significantly increased expression in flr-1(RNAi) comparing to in control RNAi animals. This is an incomplete list.

WBPaper00053254:hsp-90(RNAi)_upregulated_protein

rotein levels were obtained after comparing the isotope-tagged sample with the non-tagged sample. Averages of two experiments were calculated. A proteins was only included in the final list if several different peptides were quantified for it. Proteins with increased levels in hsp-90(RNAi) nematodes at L4 larva stage.

WBPaper00053254:hsp-90(RNAi)_downregulated_protein

rotein levels were obtained after comparing the isotope-tagged sample with the non-tagged sample. Averages of two experiments were calculated. A proteins was only included in the final list if several different peptides were quantified for it. Proteins with decreased levels in hsp-90(RNAi) nematodes at L4 larva stage.

WBPaper00040821:Au-NP_regulated

Hierarchical clustering was performed in Partek to confirm that the samples match to the treatment groups. Analysis of variance (ANOVA) was used to partition the variance due to treatment from technical and biological noise. The list of differentially expressed genes was generated by identifying the genes showing fold change of more than 1.5 and less than -1.5 at p < 0.05 with and without multiple sample correction, False Discovery Rate (FDR). False discovery correction according to Benjamini and Hochberg produced a list of 37 significant transcripts. FDR was not applied when selecting differential expressed genes, because this approach can increase the type II error and result in elimination of the genes responsive to the treatment. Genes with differeiential expression after exposed to Au-NP.

WBPaper00041876:daf-10(m79)_downreglated

Linear normalization was carried out with the Acuity 4.0 software and significance analysis using the Cyber T-test program. Genes with a p value lower than 0.02 were considered significant. The significant gene list was compared to known gene lists using the hypergeometric probability. Genes down-regulated in daf-10(m79) mutants versus wild-type animals.

WBPaper00045974:NSM_enriched_totalRNA_tiling

A linear model and moderated t-statistic were used to determine differentially expressed genes as implemented by the limma package (v3.21.4). Enriched list contains only genes significantly enriched in the NSM neurons versus the reference <=1.5X and <= 5% FDR. Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to tiling array analysis towards total RNA.

WBPaper00041876:daf-10(m79)_upreglated

Linear normalization was carried out with the Acuity 4.0 software and significance analysis using the Cyber T-test program. Genes with a p value lower than 0.02 were considered significant. The significant gene list was compared to known gene lists using the hypergeometric probability. Genes up-regulated in daf-10(m79) mutants versus wild-type animals.

WBPaper00032976:dosage_compensated_genes

Statistical analysis was performed using a moderated t-test with FDR multiple testing correction (Benjamini-Hochberg method). For each experimental strain, a separate list of genes was complied that met different sets of criteria explained in the results. Comparison of changes in gene expression between different strains was performed by comparing the lists of genes. Genes that are dosage compensated.

WBPaper00031003:total_muscle_enriched

A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets. Total muscle enriched genes (complete list of non-overlapping genes from the 0hr and 24hr muscle enriched datasets).