Large scale comparison of global gene expression patterns in human and mouse
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36 citations
Cites background or methods from "Large scale comparison of global ge..."
...coefficients) for the top n = [10, 20, 30, 50] targets of each TF in the second species (see Materials and Methods)....
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...The top 10 targets for each TF in humans (mice) were first identified, and then the overlap with the top n = [10, 20, 30, 40, 50] mouse (human) targets for the same TF was computed....
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...Second, the evidence for conservation of the top n = [10, 20, 30, 50] targets of each TF in mice (humans) was assessed in humans by using the Wilcoxon rank sum test to compare the distribution of the coexpression values for the top n targets compared with the distribution of coexpression values between that TF and all genes....
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...First, for each TF in mice (humans), the top 10 targets were defined based on coexpression values, and the overlap of these targets was assessed in the top n = [10, 20, 30, 50] targets for the same TF in human (mouse)....
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36 citations
Cites background from "Large scale comparison of global ge..."
...In addition, previous studies showed that orthologous genes were more likely to share correlated expression patterns compared with non‐orthologous genes [66,67]....
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...In addition, previous studies showed that orthologous genes were more likely to share correlated expression patterns compared with non-orthologous genes [66,67]....
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35 citations
Cites background from "Large scale comparison of global ge..."
...Likewise, the tissue-specific transcriptome of human and rodents is usually clustered based on tissue function and developmental origin (Son et al., 2005; Zheng-Bradley et al., 2010)....
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35 citations
Cites background or methods from "Large scale comparison of global ge..."
...2012) and are available as a series of meta-analysed experiments coanalysed with human orthologues of mouse genes (Zheng-Bradley et al. 2010)....
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...…data from array-based and sequencing technologies are stored in the European Bioinformatics Institute’s (EBI) gene expression atlas (Kapushesky et al. 2012) and are available as a series of meta-analysed experiments coanalysed with human orthologues of mouse genes (Zheng-Bradley et al. 2010)....
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34 citations
References
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"Large scale comparison of global ge..." refers methods in this paper
...The resulting 1,323 CEL files were pre-processed using Bioconductor’s RMA package [32] to create an integrated, normalized data matrix....
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3,513 citations
"Large scale comparison of global ge..." refers background or result in this paper
...While studies suggested that orthologous genes do not share similar expression patterns [1-5], other groups reported the opposite observations [6-9]....
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...Alternatively, many other studies made use of species-specific arrays to identify coexpressed groups of orthologous genes [4-6,16,17]....
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2,683 citations
"Large scale comparison of global ge..." refers methods in this paper
...PCA has been often used to study high-dimensional data generated by genome-wide gene expression studies [22-25]....
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2,625 citations