WBPaper00030839:Embryo_Pan_Neuronal

A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. Embryonic Pan-neural Enriched Genes.

WBPaper00030839:Larval_Pan_Neuronal

A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. Larval Pan-neural Enriched Genes.

WBPaper00030839:Embryo_A_Class

A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. Embryonic A-class motor neuron enriched genes.

WBPaper00030839:Larval_A_Class

A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. Larval A-class motor neuron enriched genes.

WBPaper00031532:Larva_Pan_Neuronal_Enriched

To identify differentially expressed transcripts, normalized intensity values from the pan-neural data sets were compared to a reference (from all larval cells) using Significance Analysis of Microarray software (SAM). A two class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the reference at a False Discovery Rate (FDR) = 3%. WT-Pico Pan-neural Enriched Genes, with genes found multiple times in a single dataset removed (without dups).

WBPaper00031532:Larva_Pan_Neuronal_Depleted

To identify differentially expressed transcripts, normalized intensity values from the pan-neural data sets were compared to a reference (from all larval cells) using Significance Analysis of Microarray software (SAM). A two class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the reference at a False Discovery Rate (FDR) = 3%. WT-Pico Pan-neural Depleted Genes, with genes found multiple times in a single dataset removed (without dups).

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.