- 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.
- WBPaper00053771:down_by_skn-1(RNAi)
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) animals comparing to vector controls.
- WBPaper00053771:up_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 increased expression in dpy-7(e88) animals comparing to N2 animals.
- WBPaper00045622:DR1345_vs_SR708_regulated
Transcript levels ascertained on microarrays were considered to display differential expression if their genome-wide false discovery rate q (the expected frequency of false positives for the entire microarray) was less than 5%; in order to further restrict the gene list, a lower threshold (e.g., q < 1% or q = 0) was sometimes used. A separate cohort was expanded and its RNA extracted for each microarray, so that the biological N was equal to the number of assays.
Genes with highly differential expression dependent on the lsq4 QTL when comparing gene expression profile between DR1345 and SR708.
- WBPaper00061210:huIs179_upregulated
Differential gene expression analysis was done with DESeq2 R-package using an FDR based on adjusted P < 0.05. (The threshold was reset from FDR < 0.1 to FDR < 0.05 by WormBase curator.)
Transcripts that showed significantly increased expression in Q neuroblast descendant cells expressing a constitutively active, N terminally truncated form of BAR-1 (beta-catenin) (del-N-BAR-1 Q) (huIs179).
- WBPaper00061210:huIs179_downregulated
Differential gene expression analysis was done with DESeq2 R-package using an FDR based on adjusted P < 0.05. (The threshold was reset from FDR < 0.1 to FDR < 0.05 by WormBase curator.)
Transcripts that showed significantly decreased expression in Q neuroblast descendant cells expressing a constitutively active, N terminally truncated form of BAR-1 (beta-catenin) (del-N-BAR-1 Q) (huIs179).
- WBPaper00053771:up_at_3h-NaCl
Authors considered genes differentially expressed if they had a q-value <= 0.05 and a b-value >= 1 or <= -1.
Transcripts that showed significantly increased expression in animals after 3 hours of exposure to 300mM NaCl comparing to control animals.