WBPaper00060871:M.humicola-infection_24h_regulated

Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1). Transcripts that showed significantly altered expression 24 hours after animals were infected by M. humicola.

WBPaper00060871:M.humicola-infection_48h_regulated

Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1). Transcripts that showed significantly altered expression 48 hours after animals were infected by M. humicola.

WBPaper00060871:M.humicola-infection_12h_regulated

Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1). Transcripts that showed significantly altered expression 12 hours after animals were infected by M. humicola.

WBPaper00060871:M.humicola-extract_1h_regulated

Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1). Transcripts that showed significantly altered expression one hour after animals were exposed to M. humicola extract.

WBPaper00060871:M.humicola-extract_24h_regulated

Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1). Transcripts that showed significantly altered expression 24 hours after animals were exposed to M. humicola extract.

WBPaper00060871:M.humicola-extract_12h_regulated

Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1). Transcripts that showed significantly altered expression 12 hours after animals were exposed to M. humicola extract.

WBPaper00060871:M.humicola-extract_4h_regulated

Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1). Transcripts that showed significantly altered expression 4 hours after animals were exposed to M. humicola extract.

WBPaper00061340:M_cell

Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm. Top 300 transcripts enriched in M cell according to single cell RNAseq.

WBPaper00050332:juglone_upregulated

Using the Cufflink package and CuffDiff application from Galaxy, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were calculated and tested for differential expression with a FDR score of 5%. Transcripts that showed significantly increased expression after exposed to 38 M juglone for 3 hours.

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.