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. 2013 Oct 18;3(12):2187–2194. doi: 10.1534/g3.113.008011

Table 1. Directional expression divergence between Malaysian and wine/European yeast in coregulated gene groups.

Group Annotation Upregulated Adjusted P
Node 7 Ribosomal proteins Malaysian <0.0001
AFT1 targets Iron homeostasis Wine/European 0.0078
Node 36 Enzymes Malaysian 0.0156
GO:0007039 Vacuolar protein catabolic process Malaysian <0.0001
GO:0006519 Cellular amino acid metabolic process Wine/European 0.0100
GO:0006725 Cellular aromatic acid metabolic process Wine/European 0.0133
GO:0006811 Ion transport Wine/European 0.0300
GO:0006082 Organic acid metabolic process Wine/European 0.0320
GO:0006826 Iron ion transport Wine/European 0.0400
GO:0055085 Transmembrane transport Wine/European 0.0400

Each row reports the results of a test for expression changes of the same sign between Malaysian and wine/European strains in one group of functionally related genes. Group indicates identifier of regulon (Gasch et al. 2004) or Gene Ontology term. Upregulated, population with elevated expression. Adjusted P indicates significance of a two-sided resampling test relative to the genomic null for an extreme value of the sum, across genes of the indicated regulon, of the signs of the log2 ratio of expression in Malaysian yeast to wine/European yeast assessed using all isolates from each population and corrected for multiple testing with the Benjamini-Hochberg method. Shown is the set of tested groups significant at adjusted P < 0.05.