- WBPaper00033101:spr-5_regulated
Significantly differentially regulated genes were selected by using a 2-fold ifference along with intensity values > 1000.
Genes regulated by spr-5 (greater than 2-fold change between spr-5(by101) generations 1, 13, and 26).
- WBPaper00055013:hmg-3(bar24)_downregulated
DESeq 2, fold change > 4, adjusted p-value < 0.05.
Transcripts that showed significantly decreased expression in BAT525 [hmg-3 (tm2539) / dpy-5(e61) unc-13(e1091) I.] comparing to in N2 at 1-day post L4 adult hermaphrodite stage
- WBPaper00055013:hmg-3(bar24)_upregulated
DESeq 2, fold change > 4, adjusted p-value < 0.05.
Transcripts that showed significantly increased expression in BAT525 [hmg-3 (tm2539) / dpy-5(e61) unc-13(e1091) I.] comparing to in N2 at 1-day post L4 adult hermaphrodite stage.
- WBPaper00048980:aging_upregulated
Proteins that significantly changed across replicates were identified using the rank product algorithm. The false discovery rate corresponding to each rank product was calculated by 10,000 random permutations of the ranks for each of the three replicates. At a 10% false discovery rate, 53 proteins significantly changed in abundance with age.
Proteins that showed signicantly increased expression in day 13 animals comparing to in day 4 animals.
- WBPaper00048980:aging_downregulated
Proteins that significantly changed across replicates were identified using the rank product algorithm. The false discovery rate corresponding to each rank product was calculated by 10,000 random permutations of the ranks for each of the three replicates. At a 10% false discovery rate, 53 proteins significantly changed in abundance with age.
Proteins that showed signicantly decreased expression in day 13 animals comparing to in day 4 animals.
- WBPaper00061527:T12G3.1_17-T12G3.1_18846
All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.
Coexpression clique No. 13, T12G3.1_17-T12G3.1_18846, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00061527:fbxb-13-fbxb-24
All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.
Coexpression clique No. 125, fbxb-13-fbxb-24, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00061527:clec-13-F35E8.10
All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.
Coexpression clique No. 179, clec-13-F35E8.10, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00028360:Phospho-Sulfo-Modified_proteins
The protein identification was performed by PMF analysis with the spectra in the positive ion mode. Database searches against all entries of Refseq Release 13 were carried out using Biotools 2.2 (Bruker Daltonics) and MASCOT search engine (Matrix Science, London, UK). The search parameters allowed carbamidomethylation of Cys, partial oxidation of Met, 150 ppm for mass tolerance, and one missed cleavage per peptide. The protein identification results were accepted in consideration of the MASCOT score. Furthermore, the reliability of the results was confirmed by the additional information of the spectrum observed in the negative ion mode.
Phosphorylation and sulfonation peptides were detected by Mass Spectrometry using the positive and negative ion modes with mono-ammonium phosphate as the matrix additive.