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Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed enhanced gene allocation for transporters (0.45 3.07%), ABC transporters (0.38 2.07%), methane (0.16 1.06%), fatty acid (0.018 0.15%), nitrogen (0.07 0.17%), butanoate (0.06 0.35%), propanoate (0.004 0.26%) metabolism and some xenobiotics (0.007 0.13%) degradation.
The module algorithm, not allowing gene allocation to modules of opposing nature, was applied to 21 microarray experiments obtained from GEO, characterised by sufficient numbers of expressed genes and presence of genes of contradicting behaviour in the same modules.
Figure 6 shows the mean number of iterations required for the algorithms to converge, while Figure 7 represents the same data in an ordered fashion from the experiment with the least number of expressed multi-membership genes and possible positions for gene allocation to the experiment with most such positions.
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In particular, we developed a methodology for estimating the similarity of two gene allocations in terms of the probability of obtaining them purely by chance.
As previously observed the, the mean number of iterations required for the algorithm to converge exhibits significant correlation of 0.9419 to the number of possible gene allocations, as does the mean fitness with correlation of 0.9616.
While the hamming distance between two multi-membership gene allocations reveals biological similarity, answering the question of how similar two allocations are the fuzzy adjusted rand index examines if each pair of genes is placed together or in different pathways by subsequent runs of our algorithms.
Sequence similarity makes sequencing of single genes and allocation of sequences into respective genomes difficult.
A gene involved in allocation of K from root to shoot was repressed (SKOR).
On the contrary, there is no significant correlation between the number of gene to pathways allocations and the mean hamming distance between allocations produced by subsequent runs of the three search algorithms, as shown on Figure 9.
Importantly, FARI remain high even for variable hamming distances, which as in the case of gene to pathways allocations suggests that in certain pairs of allocations, exhibiting substantial hamming distance, groups of genes have still been allocated together, in the same module, leading to high FARI values.
Second, our analysis of the organization of vertebrate TMC genes implied identical allocation of the individual TMCs.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com