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To explore this further, we compare sets of sensitivity- and fitness-based genetic interactions with datasets generated by Workman et al [ 12] describing MMS-induced differential gene expression and protein-DNA interactions in the presence of MMS.
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The use of visual analytics software to allow human interaction with dataset is increasingly recognized as relevant to gaining novel insights into biological datasets beyond purely biostatistical approaches.
This procedure enables users to compare their own interactions with existing datasets or to assess them by confidence servers.
Similarly, the interplay between energy and protein intakes could be important but we were not able to adequately assess these interactions with this dataset.
We conducted genome-wide two-way interaction analysis and higher-order interactions with WTCCC-BD dataset [ 19].
Hence, our contribution for this paper is at least as much the introduction of the novel MIP optimization approach to solve such problems, as it is in getting definitive results on the protein DNA interactions with the initial dataset we solved.
Meyohas mentions that archive theory is an important aspect of the project, "in a sense, each interaction with a dataset becomes a part of the archive that interaction is traced, and inscribed as additional data that can be made to offer up a second level of information".
We observe that the correlation between TIC with exclusion and median or noise level normalization factors is high (>0.91), indicating that these normalization will give similar results, without the requirement for manual interaction with the dataset.
This GPU implementation allows to conduct the search for epistatic interactions on datasets with 100s of individuals and 100 000s of SNPs in less than a day.
To generate the draft mosquito interaction network, we selected different interaction datasets with available confidence scores or rankings.
In summary, our work provides a new protein interaction degree measure by integrating protein interaction datasets with gene expression datasets.
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