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This "little used pathway" is in fact the principal walking road from the park's lake up to the Nethermead.
Yet, assessment of the most commonly used pathway to train MD/PhDs suggests that this pathway may not be the optimal way to train physician scientists to do patient-oriented research.
Therefore we used pathway mapping to identify these.
Both methods promote pathway-level comparative analysis of multiple gene lists or datasets on top of commonly used pathway enrichment analysis of a single gene list.
We used Pathway Studio 6.0 to search for genes that showed a two-fold or greater expression change in the cDNA microarray and quantitative RT-PCR experiments to see whether TNFα may directly regulate some of the genes (Figure S3).
We used Pathway Tools [ 45] to export the content of HumanCyc into flat files.
To this end, they used pathway 4 to 9 in Fig. 3.
We then used pathway analysis to further inform on the biological context for our integrated findings.
We also compared DERA with GSEA and SPIA, which are commonly used pathway analysis methods.
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Generation of affected KEGG pathways (Kyoto Encyclopedia for Genes and Genome, Kyoto University, Japan) used Pathway-Express, a web-based tool freely available as part of the Onto-Tools (http://vortex.cs.wayne.edu) [42].
In this study, we used pathway-focused low density expression cDNA arrays to screen for candidate genes related to tumor progression.
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