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This is not visible in ELEARN and MUSIC because these datasets are not large enough to completely forget similarities and frequencies.
Because these datasets are smaller than the combined dataset for all lineages, we did not attempt to jointly infer the values of the mutation rate and the mean tract length of imported sequence fragments.
Our rationale was that, because these datasets are derived from whole pieces of tissue and therefore have a significant gene-expression contribution from both stromal and nonmotile tumor cells, the highest gene-expression changes are more likely to be observed above the noise and across multiple patients.
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These datasets are chosen, because the empirical amino acid substitution rate matrices, cpREV64 [ 28], mtREV [ 6], and FLU [ 29], that were designed as those specific to the respective protein sequences are available.
Both datasets contain more one-side located domains than TOPDOM because these datasets were not filtered for transmembrane proteins and/or domains containing transmembrane regions were also included.
On the other hand, because these datasets were not generated by random efforts of the community, rather, they are likely biased to well-studied cooperative TFs, and their CRMs are relatively well documented in the literature.
These datasets were chosen because all authors, using a non-English version of the EAI worldwide, were contacted for possible collaboration.
These datasets were chosen because the experiments were performed in different laboratories but used RNA extracted from the common laboratory strain RH and expression profiling was performed on the community generated Toxoplasma chip on the Affymetrix microarray platform [ 16].
These datasets were shown to differ because of reporting bias [ 23].
Because these experimental datasets are under different conditions, we used different input sources and output biomass in the networks for the different datasets, as listed in Supplementary Files.
They are used nonetheless, because no better datasets are available.
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CEO of Professional Science Editing for Scientists @ prosciediting.com