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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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Transcripts that showed significantly increased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals. |
DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. |
WBPaper00060014:set-2(tm1630)_upregulated
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Down-regulated genes (fold change > 1.5) in two CoQ-deficient clk-1 mutant strains (e2519, qm30) compared to wild types N2. |
Fold-changes of intensities were calculated from the arithmetic mean of gene expression values between experimental and corresponding control group. Fold change >= 1.5 was used as cut-off. |
WBPaper00045774:clk-1_downregulated
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Transcripts down regulated in hpl-2(tm1489) L3 larva comparing to N2 in tiling array analysis. |
Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probe sets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction. |
WBPaper00040560:hpl-2_L3_downregulated
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Bacteria Diet: L. plantarum with pdxH mutant vs. L. plantarum |
Transcripts that showed significantly increased expression in N2 animals fed with L. plantarum with pdxH mutant, comparing to in N2 animals fed with L. plantarum. |
GFold3, logFC < -1 or > 1. |
WBPaper00066703:L.plantarum-pdxH_upregulated
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mRNAs that showed significantly increased expression in monosomal fractions in N2 comparing to in daf-2(e1370), according to RNAseq study. |
Differentially expressed genes were determined using cuffdiff across all pairs. |
WBPaper00046337:monosomal_N2_vs_daf-2_upregulated
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Transcripts that showed significantly decreased expression in VC1743[mett-10(ok2204)] comparing to in N2 when animals grow on standard (OP50) plates. |
DESeq2, p-value < 0.05, fold change > 2. |
WBPaper00061357:mett-10(ok2204)_downregulated_OP50
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