- WBPaper00029237:CUL-3_interacting
Proteins with more than 2 peptides above a score of 40 were accepted as confident matches. In the case of proteins smaller than 10 kDa, single-peptide matches were accepted after manual validation.
Proteins immunopurified with CUL-3 antibody and considered as subunits of the CSN protein complex, according to proteomics analysis.
- WBPaper00029237:CSN-5_interacting
Proteins with more than 2 peptides above a score of 40 were accepted as confident matches. In the case of proteins smaller than 10 kDa, single-peptide matches were accepted after manual validation.
Proteins immunopurified with CSN-5 antibody and considered as subunits of the CSN protein complex, according to proteomics analysis.
- WBPaper00029237:CSN-2_interacting
Proteins with more than 2 peptides above a score of 40 were accepted as confident matches. In the case of proteins smaller than 10 kDa, single-peptide matches were accepted after manual validation.
Proteins immunopurified with CSN-2 antibody and considered as subunits of the CSN protein complex, according to proteomics analysis.
- WBPaper00035227:heat_shock_regulated
Differences between treatments were visualized by principal component analysis (PCA) plotting with MeV/TM4. Data were initially filtered out for missing values and then subjected to a CLEAR test that combines differential expression and variability using the GEPAS web server at http://www.gepas.org. In our case, the false discovery rate was set to a stringent level of 5 per cent.
Genes regulated by heat shock.
- WBPaper00035227:bio-electrospray_regulated
Differences between treatments were visualized by principal component analysis (PCA) plotting with MeV/TM4. Data were initially filtered out for missing values and then subjected to a CLEAR test that combines differential expression and variability using the GEPAS web server at http://www.gepas.org. In our case, the false discovery rate was set to a stringent level of 5 per cent.
Genes regulated by bio-electrospray.
- WBPaper00053606:N2_vs_elt-7(tm840)_downregulated
RNA-seq count data were filtered for detected genes (> 10 counts across all samples) and analyzed using DESeq. 2 with Cook's cutoff filtering set to FALSE. Genes were counted as differentially expressed if they registered a Benjamini-Hochberg corrected p-value less than 0.05 and a log2-fold change greater than 1.2 between any pair-wise conditional comparison.
Genes that are down-regulated in wild-type N2 larvae compared to elt-7(tm840) larvae. In this case, no gene was downregulated.
- WBPaper00037147:heatshock_upregulated
Survival during heat stress was analyzed using a non-parametric (Mantel-Haenszel) Log rank test and presented as Kaplan-Meier survival curves (Prism software package). For the TSA analysis all full genome wide expression analyses involved comparisons of two groups and thus on a gene by gene basis, for each set, authors performed two-sample t-tests on the log2 transformed expression measures to derive raw p-values. The Benjamini and Hochberg was then used to report the inference adjusted for multiple comparisons (q-values), in their case controlling false discovery rate (FDR). Statistically significant differential expression was defined as FDR q-value <= 0.05, thereby controlling FDR at <= 0.05 for each set of comparisons. Shown here are heat shock vs control ratio and raw p_value based on two-sample t-test.
Genes for which heat shock F3 (fraction 3, containing heavy polysomes) versus control F3 is significantly increased.
- WBPaper00037147:heatshock_downregulated
Survival during heat stress was analyzed using a non-parametric (Mantel-Haenszel) Log rank test and presented as Kaplan-Meier survival curves (Prism software package). For the TSA analysis all full genome wide expression analyses involved comparisons of two groups and thus on a gene by gene basis, for each set, authors performed two-sample t-tests on the log2 transformed expression measures to derive raw p-values. The Benjamini and Hochberg was then used to report the inference adjusted for multiple comparisons (q-values), in their case controlling false discovery rate (FDR). Statistically significant differential expression was defined as FDR q-value <= 0.05, thereby controlling FDR at <= 0.05 for each set of comparisons. Shown here are heat shock vs control ratio and raw p_value based on two-sample t-test.
Genes for which heat shock F3 (fraction 3, containing heavy polysomes) versus control F3 is significantly decreased