- WBPaper00056293:rpl-5(0)-rpl-33(0)_upregulated
Limma Package. When generating the contrast matrix in limma: wildtype data was counted as wild-type and rpl-33 & rpl-5 data were both counted as RP null data. For this reason there is only one fold change value per gene as calculated by the difference between RP null RNA and wild-type RNA.
Transcripts that showed significantly increased expression in rpl-5(cc5998) vs wild type (PD1074) and rpl-33(cc2558) vs wild type (PD1074) animals.
- WBPaper00056293:rpl-5(0)-rpl-33(0)_downregulated
Limma Package. When generating the contrast matrix in limma: wildtype data was counted as wild-type and rpl-33 & rpl-5 data were both counted as RP null data. For this reason there is only one fold change value per gene as calculated by the difference between RP null RNA and wild-type RNA.
Transcripts that showed significantly decreased expression in rpl-5(cc5998) vs wild type (PD1074) and rpl-33(cc2558) vs wild type (PD1074) animals.
- WBPaper00049942:HeatShock_upregulated_hsf-1(+)
Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value).
Transcripts that showed significantly increased expression in animals injected with control vector, after heat shock at 33 C for 30min, comparing to without heat shock.
- WBPaper00049942:HeatShock_downregulated_hsf-1(+)
Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value).
Transcripts that showed significantly decreased expression in animals injected with control vector, after heat shock at 33 C for 30min, comparing to without heat shock.
- WBPaper00049942:HeatShock_downregulated_hsf-1(RNAi)
Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value).
Transcripts that showed significantly decreased expression in hsf-1(RNAi) animals, after heat shock at 33 C for 30min, comparing to in hsf-1(RNAi) animals without heat shock.
- WBPaper00049942:HeatShock_upregulated_hsf-1(RNAi)
Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value).
Transcripts that showed significantly increased expression in hsf-1(RNAi) animals, after heat shock at 33 C for 30min, comparing to in hsf-1(RNAi) animals without heat shock.
- WBPaper00061527:msp-63-msp-33
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. 86, msp-63-msp-33, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00061527:172616_x_at-172712_x_at
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. 33, 172616_x_at-172712_x_at, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00061527:sre-33-ZK1025.1_8337
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. 203, sre-33-ZK1025.1_8337, on the genome-wide coexpression clique map for the nematode GPL200 platform.