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Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. |
DESEQ2, fold change > 2 and FDR < 0.01. |
WBPaper00062103:neuron_enriched
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Genes expressed in N2. |
Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0. |
WBPaper00025141:N2_Expressed_Genes
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UVC-EtBr-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total) and exposed to EtBr (5ug/mL in agar).) vs EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) at just prior to the second UVC dose (24h). |
Genes differentially expressed under UVC exposure and EtBr treatment vs under EtBr treatment but without UVC exposure at the -25h timepoint (just prior to the second UVC dose (24h)). |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:UVC-EtBr-exposed_vs_EtBr-exposed_24h
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Genes from N2 animals with significantly increased expression after 72 hours of treatment on growth media with 10uM rapamycin in 2% DMSO. |
Analysis of gene expression data was carried out with the Affymetrix Transcriptome Analysis Console. Data preprocessing (using RMA normalization) and QC metrics were performed using Affymetrix Expression Console TM and manually inspected afterwards. Expression analysis was carried out for each two pairwise conditions. FDR statistical correction for multiple testing resulted in a slightly lower number of DEGs in most cases. P-value < 0.05 and fold change > 2.0 were used to determine differentially expressed genes. |
WBPaper00048989:N2_rapamycin_upregulated
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Genes expressed in embryonic motor neurons (identified by unc-4::GFP expressing cells). |
Genes called Present by MAS 5.0 in 2 out of 3 unc-4::GFP hybridizations. |
WBPaper00025141:unc-4::GFP_Expressed_Genes
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Genes with expression level regulated by genotype (N2 vs CB4856) at Old adults stage (214 hours at 24 centigrade). |
Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0136. |
WBPaper00040858:eQTL_regulated_old
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Transcripts that showed significantly increased expression in zcIs13; twnEx320[Punc-119-ds-fzo-1] comparing to in zcIs13[Phsp-6-gfp] animals. |
Fold change >= 1.5. |
WBPaper00061409:neuronal-fzo-1(RNAi)_upregulated
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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_17
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Genes with variation in expression level across genotypes (AB2, CB4856, RC301, CB4857, N2, HC445). |
two-way ANOVA |
WBPaper00041174:genotypic
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Genes with significant variation in expression level only across genotypes(AB2, CB4856, RC301, CB4857, N2, HC445), but not environments (control, 25C, High-pH-Salt, Liquid, infection). |
two-way ANOVA |
WBPaper00041174:genotypic_prime
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FBF-associated probe sets (FDR <2.25%) |
SAM assigns a score to each probe set and estimates their false discovery rates (FDRs). SAM deemed 4722 probe sets as significantly enriched at an FDR of 2.25% or lower. |
WBPaper00035905:FBF-1_Associated
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Genes with differential expression under 0.5mg/l Chlorpyrifos (CPF) and 1.0mg/l Diazinon (DZN) treatment at 16 centigrade. |
To identify the differentially expressed genes in each treatment authors used linear models per toxicant and temperature (gene expression = Toxicant (effect) + error). The lm function in R stats package was used to implement the linear models analysis with recommended default options. For threshold determination authors used a permutation approach. For each of the 23,232 permutations used authors randomly picked a transcript (array spot), which could only be picked once. Authors combined all the expression values of this transcript and randomly distributed them over the replicates and used them in the linear model. In this way authors obtained a threshold for each of the toxicants. Authors used a -log10 p-value 2 as common threshold for the analysis, which resembles to the following FDR per toxicant: 0.0155 for CPF at 24 centigrade, 0.0148 for DZN at 24 centigrade, 0.0168 for CPF+DZN at 24 centigrade, 0.0142 for CPF at 16 centigrade, 0.0151 for DZN at 16 centigrade, and 0.0148 for CPF+DZN, at 16 centigrade. |
WBPaper00037113:Chlorpyrifos_Diazinon_16C_regulated
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Transcripts that showed significantly increased expression in ASER neuron cells comparing to in whole animal, according to dissected single neuron RNASeq analysis. |
Fold change >= 4. |
WBPaper00050344:ASER-neuron_enriched
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Single-cell RNA-Seq cell group 94_0 expressed in neuron. |
scVI 0.6.0 |
WBPaper00065841:94_0
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Genes that showed higher expression level in ASER than in ASEL neuron by mRNA tagging. |
Intensities of spot features annotated as Bad or Not Found in the .gpr files were set to 1 to be removed from further analysis, and all of the six processed .gpr data were converted to .mev file with TIGR ExpressConverter ver. 1.7. The .mev files were processed with TIGR MIDAS ver. 2.19 with parameters set as follows: one bad channel tolerance policy as generous, with both of channel flag checked and background unchecked. The data were normalized by lowess normalization with default settings and with block and slide SD regularization. Authors then calculated log2(ASER/ASEL) ratios for each gene on the microarray. For the two pairs of dye-swapped repeats, authors calculated the mean log2(ASER/ASEL) of each repeat, so that up to four log2(ASER/ASEL) values per spot were obtained. Authors then calculated the percentile rank for each gene. Each gene spot detected more than once (18 847 spots) were subjected to MannWhitneys U test to assess whether its percentile rank values are significantly higher compared to the rest of the genes detected in the same experiments. Resulting significance levels are shown by P-values. From the P-values, false discovery rate (FDR) was further calculated by the Benjamini and Hochberg method. Statistical analyses were done by using R software version 2.9. |
WBPaper00035424:ASER_up
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