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One hundred and thirty-two genes had mouse mutant phenotype data and of these, 50 had an integument phenotype (affecting the skin and skin appendages) (P = 5.2×10−7).
A plasmid-borne copy of the deleted wild-type cheR1 gene complemented the mutant phenotype (data not shown).
Category information, such as protein motif information, mutant phenotype data, and protein localization data is combined with the functional linkage graphs using a unified probabilistic framework.
We noticed that the presence of an X-chromosomal balancer enhanced the baz mutant phenotype (data not shown), possibly explaining why other studies reported a stronger zygotic phenotype for this allele [25].
In this paper, we propose and evaluate a probabilistic approach for protein function prediction that integrates protein-protein interaction (PPI) data, gene expression data, protein motif information, mutant phenotype data, and protein localization data.
Our methodology combines PPI data, gene expression data, protein motif information, mutant phenotype data, and protein localization data, while using Gene Ontology (GO) "biological processes" terms [20] as the basis for functional annotation.
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XAO was created to standardize the annotation of gene expression, normal and mutant phenotypes data of Xenopus species.
As an alternative to rok RNAi, we dampened MLC activation by expressing a dominant negative form of Rok (RokKG) (Winter et al., 2001) and observed a similar suppression of α-spec mutant phenotypes (data not shown).
It was further required that the double-mutant phenotype data contained a sufficient number of observations that included u Δ or v Δ, such that the geometric mean of such measurements for u and for v was at least 180.
In YAGM, we collected seven kinds of datasets including TF-gene binding (TFB) data, TF-gene regulation (TFR) data, mutant phenotype (MP) data, functional annotation (FA) data, physical interaction (PI) data, genetic interaction (GI) data, and literature evidence (LE) data.
In the absence of T3, gill morphology did not change during the 7-day treatment period in normal or mutant phenotype tadpoles (data not shown).
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