- WBPaper00038060:SUMO-1_downregulated
The Linear Models for Microarray Data (Limma) package using linear model fitting for statistical testing with empirical Bayes variance smoothing procedure were applied to detection of differentially expressed genes in aex-3::His-SUMO-1 and myo-4::His-SUMO-1 nematodes when compared to N2. The obtained p values were corrected for multiple testing using Benjamini and Hochberg false discovery rate procedure. For downstream analysis, genes with FDR corrected p < 0.001 were used including 1,805 probe sets from aex-3::His-SUMO-1 versus N2 comparison (899 under- and 906 overexpressed) and 1,342 probe sets from myo-4::His-SUMO-1 versus N2 comparison (774 under and 568 overexpressed).
Genes showing < 0.5-fold down-regulated expression (p < 0.001) both in aex-3::His-SUMO-1 or myo-4::His-SUMO-1 C. elegans.
- WBPaper00038060:SUMO-1_upregulated
The Linear Models for Microarray Data (Limma) package using linear model fitting for statistical testing with empirical Bayes variance smoothing procedure were applied to detection of differentially expressed genes in aex-3::His-SUMO-1 and myo-4::His-SUMO-1 nematodes when compared to N2. The obtained p values were corrected for multiple testing using Benjamini and Hochberg false discovery rate procedure. For downstream analysis, genes with FDR corrected p < 0.001 were used including 1,805 probe sets from aex-3::His-SUMO-1 versus N2 comparison (899 under- and 906 overexpressed) and 1,342 probe sets from myo-4::His-SUMO-1 versus N2 comparison (774 under and 568 overexpressed).
Genes showing > 1.5-fold up-regulated expression (p<0.001) both in aex-3::His-SUMO-1 and myo-4::His-SUMO-1 C. elegans.
- WBPaper00061613:human-amyloid-beta_alpha-Synuclein(A53T)_downregulated
edgeR p-value < 0.01 and fold change > 4.
Transcripts that showed significantly decreased expression in animals with pan-neuronal expression of both human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP) and human alpha-Synuclein(A53T) (aex-3p-alpha-syn (A53T)), comparing to in N2 animals.
- WBPaper00061613:human-amyloid-beta_alpha-Synuclein(A53T)_upregulated
edgeR p-value < 0.01 and fold change > 4.
Transcripts that showed significantly increased expression in animals with pan-neuronal expression of both human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP) and human alpha-Synuclein(A53T) (aex-3p-alpha-syn (A53T)), comparing to in N2 animals.
- WBPaper00061613:human-alpha-Synuclein(A53T)_upregulated
edgeR p-value < 0.01 and fold change > 4.
Transcripts that showed significantly increased expression in animals with pan-neuronal expression of human alpha-Synuclein(A53T) (aex-3p-alpha-syn (A53T)), comparing to in N2 animals.
- WBPaper00035654:alpha-synuclein_regulated
TIGR Spotfinder software was used to filter unreliable spots based on Otsu's method algorithm and to convert good spots in microarray images to numerical form. Raw signal values were analyzed using mean centering to normalize signal values between channels. Signals from Alexa Fluor Dye Control probes were excluded from normalization process due their oversaturation leaving only probe intensities from C. elegans miRNAs to use in normalization. Signal intensity ratios were calculated for each signal pair yielding fold change values and p values for each miRNAs from the strain of investigation. A cutoff of 1.4 was used to detect modestly changing miRNAs.
Genes that differentially expressed in WBPaper00035654Is1[aex-3
- WBPaper00045217:prg-1_progressively_regulated
Genes with more than 2-fold change in expression level are considered differentially expressed.
Genes altered by more than 2-Fold in late versus early generation prg-1 mutants and prg-1; daf-2 mutants. Samples include prg-1(pk2290), prg-1(n4357), prg-1(tm872), prg-1(pk2290); daf-2(e1368), prg-1(pk2290); daf-2(e1370), prg-1(tm872); daf-2(e1370), prg-1(tm872); daf-2(m41).
- WBPaper00059609:malt-1_ilc-17.1_nfki-1_downregulated
Cufflinks (v2.2.1). q < 0.05.
Transcripts that showed significantly decreased expression in malt-1(db1194);npr-1(ad609) animals, in npr-1(ad609) ilc-17.1(tm5218) animals, and in npr-1(ad609) nfki-1(db1198) animals, comparing to the wild type control npr-1(ad609).