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Two A. thaliana protein sequence sources were tested: the list of 995 TFs cloned in the Y1H library (from REGIA) and the TAIR9 longest transcript proteome [ 64].
In turn, we also tested the list of false positives, for which our algorithm predicted 33 genes to be essential, in contrast to the experimental high throughput screen.
We tested the list of validated targets for statistical enrichment of GO categories and pathways, using the initial 21,121 screened genes/factors as a reference (Table S3).
We tested the list of significantly positive and negative correlated genes for enrichment in functional annotation groups as defined in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases [ 28].
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We then tested the lists of induced and repressed genes for overrepresentation of GO terms by applying the exact Fisher's test.
Patient interviews were performed to test the list of concepts and to collect patient responses in their own wording to create the items of the questionnaire.
Each page is firstly tested against the list of our issues, as defined in Table A3.
Next, we tested whether the list of significant pathways as defined by the LS statistic (P < 0.05) was enriched for PKA-related pathways using Fisher's Exact test.
The genes in different clusters also tested against the list of genes differentially expressed in IM, SPEM and both IM and SPEM from the recent publication by Lee et al. 2010 [ 16].
We tested the whole list of complex-disease related genes from the Global Set (n = 403) versus the NCBI full set of genes.
It then tests if the list of ranked genes is significantly enriched for pre-defined groups of genes, or "gene sets".
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