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The RiceXPro database in particular provides a large collection of expression data on japonica (Sato et al. 2013).
To extend the collection of expression data, we additionally searched animal studies of gene expression that examined depression-like behaviors in mice [11].
However, since the E. coli dataset is a collection of expression data compiled from experiments carried out in different laboratories, there may be some redundancy among these experiments or some bias in their selection.
We used the tissue body index data set, a collection of expression data of human tissues as an illustrative example.
These results strongly suggest that a comprehensive analysis of bacterial genomes requires the combination of mathematical predictions with the collection of expression data.
For our study, we employed the UniGene database, which contains comprehensive coverage of various organisms and a collection of expression data.
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It currently hosts a large collection of expression-sequence-tags (EST), unigenes, and their annotations, and integrated comparative analysis results from five other invertebrate species whose genomic information has become available from large-scale genomic studies, including the silkworm, the honeybee, the fruit fly, the mosquito, and the nematode.
We integrate two collections of expression sets, which reduce the number of possible genes to use as explanatory variables further; down to 4140 genes (since the numbers differ across the experiments, and we only utilize those genes for which we have measurements in all experiments).
The "transcriptional modules" were inferred based on a large collections of expression data in S. cerevisiae (Ihmels et al. 2002).
We have recently confirmed this hypothesis through the meta-analysis of large collections of expression data derived from many different populations of mouse cells [ 23, 24], pig tissues [ 25] and clinically derived samples [ 26].
Interest has now extended to identifying transcriptional modules across more extensive collections of expression data [ 36- 41] as well as to the application of network theory and analysis to reconstruct gene regulatory networks [ 42- 47].
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