Their similarity score is derived from pathway similarity based on pathway components (see reference for details).
HUMAnN uses an integer optimization algorithm that conservatively computes a parsimonious minimum set of reactions along KEGG pathways based on pathway presence, absence or completion [ 6, 7].
We recently developed an integrated pathway database, PathwayAPI [ 3], which utilises a novel pathway merging approach based on pathway name matches (Longest Common Substring matching; LCS) [ 3].
Among the pathway subgroups based on pathway hierarchy 2 (Additional file 3), the pathway of Ribosome was the most unigenes (662), followed by Carbohydrate metabolism 328), Biosynthesis of amino acids 327), Protein processing in endoplasmic reticulum (288) (Additional file 3).
Through the multi-step approach, 72 miRNA-mRNA pairs containing 22 dysregulated miRNAs and their 58 target mRNAs in CRC were identified, and the Wnt signaling pathway was the only affected pathway based on pathway analysis for the miRNA targets.
Besides comparing the quality of the two host-pathogen PPI datasets predicted by the two approaches based on pathway enrichment, we also analyze the pathway enrichments for the M. tuberculosis H37Rv proteins.
When summarised based on pathway classes, it was noted that pathways in lipid metabolism, the metabolism of terpenoids and polyketides, folding, sorting and degradation, and glycan biosynthesis and metabolism were the most significant (q-value < 0.1) and these were all under-expressed relative to dietary treatment D1.
Based on pathway enrichment analysis, we identified a few pathways which presented a positive monotone trend during the gestational age; most of them are involved in host immunity.
To generate a unified ranking of strains based on user-defined pathways, pathway activity aggregation is performed.
Due to the fact that, in general, mass spectrometric measurement of low abundance proteins is extremely sparse, we developed a metaprotein analytic approach for the analysis of pathway specific phosphorylation changes, based on pathways from MSigDB.
Plastid enzymes were grouped into metabolic pathways, based on pathways shown in the ExPASy biochemical pathways [ 99, 100], information from BRENDA [ 101, 102], and many references cited in the text.
