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The homozygous minimal medium classifications were used in this analysis to allow identification of knockouts that do no affect growth even when no copies are present and growth conditions are less favorable.
Thus, signals from neighboring cells of the same cell type do not increase the i-th cell's inner state, while signals from different cell types increase the i-th cell's inner state and both cavity and medium classifications increase the i-th cell's inner state even more.
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In addition, analysis of precision-recall plots (Figure 2) showed that, initially, all models occupied the region of medium classification effectiveness with high recall and low precision (quarter IV).
The default annotation category for biological processes of GO (GOTERM_BP_FAT) and the medium classification stringency settings were selected.
For the gene functional annotation clustering, the Database for Annotation, Visualization and Integrated Discovery (DAVID), fifth version (http://david.abcc.ncifcrf.gov/gene2gene.jsp) was used, with the default parameters at medium classification stringency.
To assess whether the differentially expressed genes are related to development and organogenesis, we classified the 1011 differentially expressed genes into gene ontology (GO) groups using DAVID (Database for Annotation, Visualization and Integrated Discovery) with medium classification stringency.
Medium classification stringency was used.
When performing the classification analysis, we applied the medium classification stringency, implemented Benjamini multiple testing correction and set the threshold value of Enrichment score at 1.0 [ 34].
P-values were calculated at medium classification stringency using a modified Fisher's exact test (EASE score), and terms with P-values of < 0.05 were considered significantly enriched.
The Functional annotation analysis was performed in the David Functional Annotation Clustering Analysis website (http://david.abcc.ncifcrf.gov/home.jsp), using the default setting of the medium classification stringency.
The suppressors were analyzed for GOTERM_BP_5 and GOTERM_CC_5 through functional annotation clustering using medium classification stringency with a similarity threshold of 0.50.
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