- WBPaper00039866:SAM_daf-19_downregulated
Lists of genes were generated using SAM (version 2.2) with a false discovery rate (FDR) of less than or equal to 5% (Q-value <= 5%). Twenty-seven repeated runs of SAM were performed using variable random seed numbers for each run. During each run of SAM, 100 permutations were performed. Genes (n =129 downregulated, n = 1 upregulated) appearing in at least 80% of all twenty-seven runs of SAM were further considered for signal variation filtering, which was used to selectively identify genes with a 1.5-fold or greater variation between the two genetic conditions used for comparison.
Candidate daf-19 down regulated genes with a statistically significant signal variation of 1.5-fold or greater. These were identified using a Significance Analysis of Microarrays (SAM).
- WBPaper00039866:SAM_daf-19_upregulated
Lists of genes were generated using SAM (version 2.2) with a false discovery rate (FDR) of less than or equal to 5% (Q-value <= 5%). Twenty-seven repeated runs of SAM were performed using variable random seed numbers for each run. During each run of SAM, 100 permutations were performed. Genes (n =129 downregulated, n = 1 upregulated) appearing in at least 80% of all twenty-seven runs of SAM were further considered for signal variation filtering, which was used to selectively identify genes with a 1.5-fold or greater variation between the two genetic conditions used for comparison.
Candidate daf-19 up regulated genes with a statistically significant signal variation of 1.5-fold or greater. These were identified using a Significance Analysis of Microarrays (SAM).
- WBPaper00046217:mev-1(kn1)_downregulated
The error threshold for peptide spectrum matches was set to a 1% false discovery rate (FDR). Protein expression was measured by the total of identified spectral counts normalized by the total number of spectral counts in each MS run in order to adjust for the variation in signal across runs.
Proteins that showed decreased expression in mev-1(kn1) comparing to in N2, according to liquid chromatography and mass spectrometry analysis.
- WBPaper00046217:gas-1(fc21)_upregulated
The error threshold for peptide spectrum matches was set to a 1% false discovery rate (FDR). Protein expression was measured by the total of identified spectral counts normalized by the total number of spectral counts in each MS run in order to adjust for the variation in signal across runs.
Proteins that showed increased expression in gas-1(fc21) comparing to in N2, according to liquid chromatography and mass spectrometry analysis.
- WBPaper00046217:clk-1(qm30)_upregulated
The error threshold for peptide spectrum matches was set to a 1% false discovery rate (FDR). Protein expression was measured by the total of identified spectral counts normalized by the total number of spectral counts in each MS run in order to adjust for the variation in signal across runs.
Proteins that showed increased expression in clk-1(qm30) comparing to in N2, according to liquid chromatography and mass spectrometry analysis.
- WBPaper00046217:mev-1(kn1)_upregulated
The error threshold for peptide spectrum matches was set to a 1% false discovery rate (FDR). Protein expression was measured by the total of identified spectral counts normalized by the total number of spectral counts in each MS run in order to adjust for the variation in signal across runs.
Proteins that showed increased expression in mev-1(kn1) comparing to in N2, according to liquid chromatography and mass spectrometry analysis.
- WBPaper00046217:gas-1(fc21)_downregulated
The error threshold for peptide spectrum matches was set to a 1% false discovery rate (FDR). Protein expression was measured by the total of identified spectral counts normalized by the total number of spectral counts in each MS run in order to adjust for the variation in signal across runs.
Proteins that showed decreased expression in gas-1(fc21) comparing to in N2, according to liquid chromatography and mass spectrometry analysis.
- WBPaper00046217:clk-1(qm30)_downregulated
The error threshold for peptide spectrum matches was set to a 1% false discovery rate (FDR). Protein expression was measured by the total of identified spectral counts normalized by the total number of spectral counts in each MS run in order to adjust for the variation in signal across runs.
Proteins that showed decreased expression in clk-1(qm30) comparing to in N2, according to liquid chromatography and mass spectrometry analysis.
- WBPaper00059567:olrn-1(ums9)_regulated
The Ballgown package from the Bioconductor software suite (version 3.8) was used to run a custom R script in R console(R Version 3.5) to analyze the differential gene expression, visualize the data, and perform statistical tests for differential expressionwith multiple test correction. A gene was considered to be differentially regulated if its fold change versus wild-type was greater thantwo, the adjusted p value was less than 0.05, and its RPKM was greater than one.
Transcripts that showed significantly altered expression in olrn-1(ums9) comparing to in N2 animals.