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Although less serious, the small pathway sizes constitute yet another problem.
A set of 1050 S. cerevisiae pathways was obtained from CPDB and processed to remove data duplication and reduce the range of pathway sizes (pathway sizes in the original data set ranged from 1 to 310).
Then the median pathway sizes are joined to show the overall trend between size and rank (Additional file 2).
This study highlights substantial mutual discrepancies among different pathway sources, e.g. with regard to pathway sizes, names and gene contents.
On the other hand, some sources (e.g. HumanCyc, PID and PharmGKB) have very little variation in their pathway sizes, revealing their focus on pathways of particular size.
One of the advantages for methods using raw genotypes is that permutation can be used to account for LD between SNPs and to correct for gene or pathway sizes.
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Default settings were used except the maximum and minimum pathway size exclusion criteria were set to 1,000 and 5, respectively.
The lack of kinetic data has limited the size of the modeled networks to pathway size, with exception for the human red blood cell model (Jamshidi et al. 2001).
Note, the metric (see Materials and Methods) compensates for pathway size.
It should be noted that pathway size distribution is not a measure of accuracy of our method.
It is necessary to determine optimal values for pathway size, completeness, and how the sizes of each pathway in a compensatory pathway pair are balanced.
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