WBPaper00041370:spg-7(RNAi)_upregulated_atfs-1_dependent

Data normalization, scaling and 2 -way Anova was used to identify differentially expressed genes, using Partek Geno mics Suite (v6.5). Average linkage gene clustering was performed with a Euclidean distance using Hierarchical clustering. The genes with statistically significant changes between the treatments and strains were identified using Anova streamlined (Partek Genomic Suite (v6.5)). Only genes with a fold change higher than 1.3 and p-value lower than 0.05 were considered. Genes up-regulated during spg-7(RNAi) treatment that are dependent on atfs-1(tm4525).

WBPaper00049538:atfs-1(et18)_upregulated

Differences in gene expression between N2 and atfs-1(et18) worms was determined using Anova streamlined (Partek Genomic Suite (v6.5)). Transcripts up regulated by atfs-1(et18)

WBPaper00053771:down_by_skn-1(RNAi)_at_dpy-7(e88)

Authors considered genes differentially expressed if they had a q-value <= 0.05 and a b-value >= 1 or <= -1. Transcripts that showed significantly decreased expression in skn-1(RNAi);dpy-7(e88) animals comparing to dpy-7(e88) vector controls.

WBPaper00056284:ints-7(RNAi)_downregulated

DESeq2 and edgeR. Transcripts that showed significantly decreased expression in ints-7(RNAi) comparing to in N2.

WBPaper00056284:ints-7(RNAi)_upregulated

DESeq2 and edgeR. Transcripts that showed significantly increased expression in ints-7(RNAi) comparing to in N2.

WBPaper00055941:atfs-1(et15)_downregulated

EdgeR v. 3.20.2, fold change > 2. Transcripts that showed significantly decreased expression in atfs-1(et15) comparing to in N2.

WBPaper00055941:atfs-1(gk3094)_downregulated

EdgeR v. 3.20.2, fold change > 2. Transcripts that showed significantly decreased expression in atfs-1(gk3094) comparing to in N2.

WBPaper00055941:atfs-1(gk3094)_upregulated

EdgeR v. 3.20.2, fold change > 2. Transcripts that showed significantly increased expression in atfs-1(gk3094) comparing to in N2.

WBPaper00055941:atfs-1(et15)_upregulated

EdgeR v. 3.20.2, fold change > 2. Transcripts that showed significantly increased expression in atfs-1(et15) comparing to in N2.

WBPaper00055941:nuo-6(qm200)\;atfs-1(gk3094)_upregulated

EdgeR v. 3.20.2, fold change > 2. Transcripts that showed significantly increased expression in nuo-6(qm200);atfs-1(gk3094) comparing to in N2.