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This breadth of expression precluded drawing a direct relationship between expression and phenotype, as effects of expression in other clusters cannot be ruled out with the existing dataset.
Furthermore, a few overexpression and mutant plants with the AG, SEP3, and FUL fused to eGFP were analyzed for fluorescence and confirmed the same linkage between expression and phenotype.
To establish connections between expression and phenotype data, Hoehndorf et al. (13) suggested the hypergeometric distribution for 'absent/present' calls in the expression data, in accordance with the extended FUNC software applied (22).
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To determine the relationship between gene expression and phenotype, phenotypic values from the same biological replicate measured for gene expression were correlated with the normalized gene expression values using the multivariate Pearson correlation function of JMP 7.0 (SAS Institute, Cary, NC).
The ability of pathway phenotypes to provide reliable measures of expression with direct biological interpretation means they could also be applied in these situations to understand the relationship between expression and such phenotypes.
This variation can be particularly useful for ecological studies: the accumulation of transcripts of the targeted gene can be quantified in several independently transformed lines, not only to demonstrate that the targeted gene was in fact silenced but also to examine the quantitative relationship between gene expression and phenotype.
This discrepancy between temporal expression and phenotype is attributed to three possible mechanisms.
Having established a correlation between P450 SU1 expression and phenotype, a more detailed analysis of OCP growth and development was conducted.
Furthermore, these methods of observing spatiotemporal patterns of gene expression do not prove a causal relationship between gene expression and phenotype (Hoekstra and Coyne 2007).
After enriching for inflorescence expression, the expression profile of each MPSS library was characterized to reveal relationships between gene expression and phenotype and delineate possible biases among the data.
An analysis of the correlation between gene expression and phenotype parameters was carried out using the Spearman correlation coefficient and the associated statistical test, followed by a correction of the multiplicity using Benjamini and Hochberg procedure.
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