Fig 1.
Mapping Reactome pathways elements to WikiPathways pathway elements.
This diagram shows the symbols used to represent different biological entities in Reactome and the corresponding symbol used to represent the same biological entity in WikiPathways.
Fig 2.
A comparative view of the Abacavir transport and metabolism pathway for Homo sapiens from Reactome Database (version 54).
(a) Reactome View of Abacavir transport and metabolism (Homo sapiens) [32] and (b) Pathway view on WikiPathways(WP2712_r83598) [33].
Fig 3.
Venn diagrams showing coverage of other external databases by WikiPathways and Reactome.
(a) Venn Diagram showing coverage of Gene Ontology Terms by Gene Products of WikiPathways and Reactome, (b) Venn Diagram showing coverage of Biological Process (BP), Molecular Function (MF), and Cellular Compartment (CC) Gene Ontology Terms by Gene Products of curated and reactome_approved collections of WikiPathways pathways, and (c) Venn Diagram showing coverage of the Human Metabolome Database (HMDB) by metabolites curated and reactome_approved collections of WikiPathways pathways.
Table 1.
Summary of the Gene Ontology Term Coverage.
Fig 4.
Human granulosa cells gene expression in normal ovulatory versus PCOS women visualized on the Toll-Like Receptors Cascades pathway (WP2775_r83597) in PathVisio [44].
Human granulosa cells were isolated from ovarian aspirates of normal ovulatory and PCOS women undergoing IVF. For each sample, RNA was extracted and hybridized to an Affymetrix Gene Chip. Genes not measured appear in gray. The log fold change (logFC) is depicted with a blue to yellow color gradient corresponding to the values -2 to 2. Significant genes with a P.value < 0.05 are marked in green and the rest in red. Significant complexes with a score > 25 are marked in orange and the rest in dark gray.
Table 2.
Table showing the top ten pathways obtained performing over-representation analysis in PathVisio.
Fig 5.
Conversion of Reactome Java data classes to corresponding WikiPathways Java data classes.
Fig 6.
A comparative view of hyperedges in a Reactome pathways and how they are converted in WikiPathways.
A hyperedge from the Abacavir transport and metabolism pathway is shown. (a) Reactome View (b) WikiPathways view, the anchors are highlighted.