- 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).
- WBPaper00056073:R24_upregulated_nhr-86_dependent
N.A.
Transcripts that were induced after treatment by immunostimulatory xenobiotic R24 (a.k.a RPW-24, 2-N-(3-Chloro-4-methylphenyl)quinazoline-2,4-diamine)), and the induction level was altered in nhr-86(tm2590) and nhr-86(ums12) animals.
- WBPaper00024245:gst-5-binding_control
Database searches using the monoisotopic peptide masses were undertaken using the Protein Prospector V3.2.1 MS-Fit program . Peptide modifications allowed during the search were: carboxymethylation of cysteines, oxidation of methionines, acetylation of peptide N-terminus and modification of peptide N-terminal Glu to pyroGlu. The maximum number of missed cleavages was set to 1 and the mass tolerance was limited to either 20 or 50 ppm.
Proteins that physically interact with GST-5 in N2 control condition, according to proteomic study after affinity purification, 2D-electrophoresis.
- WBPaper00057288:Cold_downregulated_protein
Two-tailed Student's t-test (n=3, P-value <0.05 was considered significant).
Proteins that showed significantly decreased expression in CF512 (fer-15(b26)II;fem-1(hc17)IV) treated with empty RNAi vector at 15C comparing to at 20C.
- WBPaper00024245:gst-5-binding_ROS-stressed
Database searches using the monoisotopic peptide masses were undertaken using the Protein Prospector V3.2.1 MS-Fit program . Peptide modifications allowed during the search were: carboxymethylation of cysteines, oxidation of methionines, acetylation of peptide N-terminus and modification of peptide N-terminal Glu to pyroGlu. The maximum number of missed cleavages was set to 1 and the mass tolerance was limited to either 20 or 50 ppm.
Proteins that physically interact with GST-5 in ROS (reactive oxygen stressed) condition, according to proteomic study after affinity purification, 2D-electrophoresis.
- WBPaper00057288:iff-1(RNAi)_upregulated_protein
Two-tailed Student's t-test (n=3, P-value <0.05 was considered significant).
Proteins that showed significantly increased expression in iff-1(RNAi) animals comparing to CF512 (fer-15(b26)II;fem-1(hc17)IV) animals applied with control vector at 15C.
- 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