From these perspectives, we first generated a reference pathway profile as the benchmark where a pathway is enriched only if it is enriched in more than one data set.
Furthermore, each organism-specific pathway is derived from a reference pathway map.
The Pathway tools software contains algorithms that predict metabolic pathways of an organism from its genome by comparison to a reference pathways database known as MetaCyc [88].
Gene symbols were used as identifiers and the Ingenuity Knowledge Base gene was used as a reference for pathway analysis.
We recognize that guidelines cannot be enforced; they serve rather as a reference and pathway for ethically conscious professionals in our field who are seeking to improve the integrity of their research or to resolve ethical challenges that they face in their work.
Using Arabidopsis thaliana as a reference for pathways analysis, we annotated and mapped 27,042 of 83,493 unigenes (32.4%) to EC numbers in 119 KEGG pathways.
As a result, the reference pathway map contains 1572 metabolite nodes and 1813 enzyme nodes.
As seen in Table 2, pathway 3 ('Lay/consultation discontinuity') was clearly associated with an increased likelihood of late referral in comparison to 'Regular source of care continuity', chosen as the reference pathway.
Just as AlzGene for risk-gene reference database, AlzPathway serves as a pathway "reference" integrating wealth of pathway information published before.
