- WBPaper00065623:46
CellRanger, DecontX, Monocle3, Louvain algorithm.
Single-cell RNA-Seq cell group 46 expressed in: SIB.
- WBPaper00061527:pqn-42_3632-pqn-42_9157
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. 8, pqn-42_3632-pqn-42_9157, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00046548:dafachronic-acid_downregulated
To identify the differentially expressed genes, we applied Significance Analysis of Microarrays (SAM) analysis using the R package samr [46]. Genes with median false discovery <5% and fold changes >2.0 were considered differentially expressed.
Genes that showed significantly decreased experssion after 22.5 hours of treatment in 200nM delta7-dafachronic acid comparing with in ethanol vehicle control.
- WBPaper00046548:dafachronic-acid_upregulated
To identify the differentially expressed genes, we applied Significance Analysis of Microarrays (SAM) analysis using the R package samr [46]. Genes with median false discovery <5% and fold changes >2.0 were considered differentially expressed.
Genes that showed significantly increased experssion after 22.5 hours of treatment in 200nM delta7-dafachronic acid comparing with in ethanol vehicle control.
- WBPaper00061527:pqn-31-ttr-21
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. 26, pqn-31-ttr-21, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00061527:pqn-54-abu-9
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. 298, pqn-54-abu-9, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00061527:K05C4.4-fbxc-46
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. 300, K05C4.4-fbxc-46, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00061527:ccpp-1_2984-C17E4.6_2397
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. 46, ccpp-1_2984-C17E4.6_2397, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00044005:DAF-16_upregulated
Authors reanalyzed raw genome-wide expression data from five studies (McElwee et al., 2003; McElwee et al., 2004; Murphy et al., 2003; Shaw et al., 2007; Troemeletal.,2006) encompassing 75 genome-wide expression profiles, which authors used to construct 46 explicit contrasts between conditions with differing levels of DAF-16 activity. After complete reprocessing of the raw data (array-specific standardization, normalization, and remapping of probes), a log-fold-change and corresponding standard error were calculated for each transcript on each array (or array pair for single-channel technologies). Together, these were converted into a vote value between 1 (highly likely to be downregulated) and +1 (highly likely to be upregulated). The total voting score for each gene was computed as the sum of voting scores for individual experiments, which is robust in the sense that the influence of any individual experiment is limited to a single full vote. An empirical null distribution based on random permutation was created, and all genes were ranked from consistently upregulated (class I) to consistently downregulated (class II). The area under the null distribution (p value) for each gene that served as the basis for assigning genes to class I or class II at a 5% false discovery rate.
Top 50 up regulated genes by DAF-16 based on reanalysis 75 previously published experiments.