- WBPaper00044501:gld-1_let-7_regulated
N.A.
Proteins that showed differential expression in (B) let-7(mg279);[let-7 sponge] when comparing to (A) [let-7 sponge], and in (C) gld-1(op236); let-7(mg279);[let-7 sponge] when comparing to (A) [let-7 sponge]
- WBPaper00058955:heatshock_upregulated_CE
DESeq2 v 1.18.1, fold change > 2, FDR < 0.01.
Transcripts that showed significantly increased expression in L2 larva stage C. elegans animals after incubated in a 34C water bath for 30min.
- WBPaper00060852:Benzo[a]pyrene_upregulated
A student t test was conducted for each comparison after quantile normalization and log2-transformation. A gene was selected if the p value was < 0.05 and the fold-change of normalized RPKMs was > 2.
Transcripts that showed significantly increased expression after L1 stage animals were exposed 48 hours at 20 C to benzo[a]pyrene supplemented to both the agar medium and the food source (E. coli OP50).
- WBPaper00039851:Live_C_albicans_vs_HK_C_albicans
Data were analyzed using Resolver Gene Expression Data Analysis System, version 5.1 (Rosetta Inpharmatics). Three biologic replicates per condition were normalized using the Resolver intensity error model for single color chips. Conditions were compared using Resolver to determine the fold change between conditions for each probe set and to generate a P value using a modified t-test. Probe sets were considered differentially expressed if the fold change was 2-fold or greater (P < 0.01). When comparing datasets, the overlap expected by chance alone was determined in 50 groups of randomly selected C. elegans genes using Regulatory Sequence Analysis Tools (http://rsat.ulb.ac.be/rsat/), a technique that has been used for similar analyses. P values were determined using chi-square tests.
Differentially expressed genes in the following exposure comparison:live C. albicans versus heat-killed C. albicans.
- WBPaper00042561:smg-2(RNAi)_downregulated
Bioconductor package LIMMA was used to determine differentially expressed genes. The P-values were adjusted for multiple testing with a false-discovery rate (50). Probe sets with fold-change > 1.5 and q-value < 0.05 were used as a cut-off for C. elegans microarrays
Genes with significant decrease of expression in UPF1 smg-2(RNAi) comparing to control.
- WBPaper00042561:smgl-2(RNAi)_downregulated
Bioconductor package LIMMA was used to determine differentially expressed genes. The P-values were adjusted for multiple testing with a false-discovery rate (50). Probe sets with fold-change > 1.5 and q-value < 0.05 were used as a cut-off for C. elegans microarrays
Genes with significant decrease of expression in DHX34 smgl-2(RNAi) comparing to control.
- WBPaper00042561:smg-2(RNAi)_upregulated
Bioconductor package LIMMA was used to determine differentially expressed genes. The P-values were adjusted for multiple testing with a false-discovery rate (50). Probe sets with fold-change > 1.5 and q-value < 0.05 were used as a cut-off for C. elegans microarrays
Genes with significant increase of expression in UPF1 smg-2(RNAi) comparing to control.
- WBPaper00042561:smgl-2(RNAi)_upregulated
Bioconductor package LIMMA was used to determine differentially expressed genes. The P-values were adjusted for multiple testing with a false-discovery rate (50). Probe sets with fold-change > 1.5 and q-value < 0.05 were used as a cut-off for C. elegans microarrays
Genes with significant increase of expression in DHX34 smgl-2(RNAi) comparing to control.