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)

WBPaper00038168:lin-35_downregulated

For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis. Genes that were downregulated in lin-35.

WBPaper00038168:lin-35_upregulated

For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis. Genes that were upregulated in lin-35.

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.