Ficklin et al.[ 29], however, used a network alignment method called IsoRankN [ 21], which combines both ortholog and topology information, to align co-expression networks of O. sativa and Zea mays.
Using a network of tissue-tissue similarities computed using their transcriptional profile, we show that our network alignment p-values are consistent with groupings derived from transcriptional signatures.
NetAligner [ 7], a recent web server, allows the comparison of user-defined networks or whole interactomes within a set of fixed species using a heuristic network alignment with no guarantees on the optimality of the identified solutions.
Although the KEGG database provides pathways under detailed metabolism categories, such as Glycerolipid metabolism and Tryptophan metabolism among many others, directly using these pathways in a network alignment study does not reveal enough information.
Of course, since the true alignment is not known, the accuracy of a network alignment A cannot be measured using (1), hence we cannot directly use this measure to compare different potential alignments to choose the best one.
They should also explain what a network alignment algorithm is.
Traditional homology transfer using a protein-protein network alignment approach [ 46- 54] does not appear feasible to predict functional othologs in the malaria parasite, because of the remote homology between P. falciparum and other known model organisms: BLAST-based sequence similarity search was unable to make functional annotation for over 60% of the genes in P. falciparum [ 11].
- Missing references concerning the available PPI datasets, the most important alignment methods and the importance of using network alignment were added.
We tested our new similarity measure using the MAS network alignment algorithm.
We refer to the most conserved subset of housekeeping genes between humans and yeast, computed using network alignment of tissues-specific networks with the yeast network, as the core genes.
