The network character of metabolic systems can be instrumental in developing concepts of agreement between expression data and pathways.
In agreement, partner pathways and mechanisms, too, have been shown to play a role in modulating transcriptional expression of the Sprouty proteins.
Analysing statistical measures of inter-annotator agreement between 98 pathways and 993 GOBP terms, we established a graph BipartiteGraphPathwayGOBP with 544 vertices, containing 96 pathways 448 associated GOBPs, and 973 edges.
We examine the agreement among the different pathway databases in three aspects: (i) agreement of genes and gene pairs in different databases, (ii) agreement of the pathways in different databases, and (iii) agreement of genes and gene pairs of the same pathway in different databases.
Demonstrating the validity of the gene signatures, we observe a large degree of agreement between pathways with predicted activity and results from previous investigations.
In agreement, metabolic pathways of progesterone are affected by modifications in the level of gonadal hormones and by pathology or injury with a regional specificity and in a sex-dimorphic way.
After we have obtained the pathway-gene and pathway-gene pair relationships from different pathway databases, agreement among the databases can be analyzed.
After obtaining the normalized pathway-gene and pathway-gene pair relationships, we are able to analyze the comprehensiveness and agreement among the different pathway databases on different aspects.
Phylogenetic relationships established by sequence types were in agreement with evolutionary pathways suggested by LSPs [14] and by SNPs in the putative DNA repair genes mutT2, muT4 and ogt [15] (Figure 1B and 1C).
The L. hongkongensis genome possesses the pentose phosphate and gluconeogenesis pathways and tricarboxylic acid and glyoxylate cycles, but incomplete Embden-Meyerhof-Parnas and Entner-Doudoroff pathways, in agreement with its asaccharolytic phenotype.
