- WBPaper00035892:Y.pestis_regulated
ANOVA t-test and fold-change calculations were performed using GeneSpring software.
Genes changed expression level after Y. pestis KIM5 treatment. P-value < 0.05.
- WBPaper00045865:biofilm_upregulated_A
Results are presented as the relative up- or downregulation for genes with a difference of 2 fold or more after analyzing expression and using confidence limits with multiple testing corrections (Benjamini-Hochberg FDR).
Genes that significantly increased expression 1 our after biofilm was formed by Y. pseudotuberculosis YP III comparing to worms infected by Y. pseudotuberculosis 3384 mutant (that do not form biofilm)
- WBPaper00045865:biofilm_downregulated_A
Results are presented as the relative up- or downregulation for genes with a difference of 2 fold or more after analyzing expression and using confidence limits with multiple testing corrections (Benjamini-Hochberg FDR).
Genes that significantly decreased expression 1 our after biofilm was formed by Y. pseudotuberculosis YP III comparing to worms infected by Y. pseudotuberculosis 3384 mutant (that do not form biofilm)
- WBPaper00035892:KIM5_vs_OP50_Down
ANOVA t-test and fold-change calculations were performed using GeneSpring software.
Genes down-regulated greater than 2-fold, demonstrating a robust inducible response to Y. pestis.
- WBPaper00035892:KIM5_vs_OP50_Up
ANOVA t-test and fold-change calculations were performed using GeneSpring software.
Genes up-regulated greater than 2-fold, demonstrating a robust inducible response to Y. pestis KIM5.
- WBPaper00045865:biofilm_downregulated_B
Results are presented as the relative up- or downregulation for genes with a difference of 2 fold or more after analyzing expression and using confidence limits with multiple testing corrections (Benjamini-Hochberg FDR).
Genes that significantly decreased expression 1 our after biofilm was formed by Y. pseudotuberculosis YP III comparing to worms infected by Y. pseudotuberculosis del-ypsI/ytbI mutant (that do not form biofilm)
- WBPaper00045865:biofilm_upregulated_B
Results are presented as the relative up- or downregulation for genes with a difference of 2 fold or more after analyzing expression and using confidence limits with multiple testing corrections (Benjamini-Hochberg FDR).
Genes that significantly increased expression 1 our after biofilm was formed by Y. pseudotuberculosis YP III comparing to worms infected by Y. pseudotuberculosis del-ypsI/ytbI mutant (that do not form biofilm)
- WBPaper00061340:Y
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 Y cell according to single cell RNAseq.
- WBPaper00041207:CE_dauer_down
The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function. Control of FDR was employed as correction for multiple testing.
Genes dowm regulated in the dauer versus dauer-exit worms.