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- Pathway Commons: A Resource for Biological Pathway Analysis
Pathway Commons aims to collect and disseminate biological pathway and interaction data Data is collected from partner databases and is represented in the BioPAX standard
- Pathway Guide · Home
Identify altered pathways within platelet RNA-Seq data using Gene Set Enrichment Analysis and visualize results in an Enrichment Map Filed under Pathway Enrichment Analysis
- PC formats - Pathway Commons
To make it easier to use all of the pathway information in Pathway Commons with typical network analysis tools, we developed a set of rules to reduce BioPAX interactions to pairwise (or binary) relationships
- Identify Pathways · Pathway Guide
Typically, a ‘pathway’ refers to gene set components that enact a change or product (e g signal transduction, metabolism) In this section we discuss the use of Gene Set Enrichment Analysis (GSEA) to sift out pathways from the underlying alterations in gene expression (Figure 1)
- Gene Set Enrichment Analysis · Pathway Guide
In this section we discuss the use of Gene Set Enrichment Analysis (GSEA) to identify pathways enriched in ranked gene lists, with a particular emphasis on ordering based on a measure of differential gene expression
- Fishers Exact Test · Pathway Guide
In general, enrichment methods require a collection of candidate sets of genes with shared attributes, for instance membership in a pathway or location on a chromosome
- RNA-Seq to Enrichment Map · Pathway Guide
This raw data will be converted into a single gene list where genes are assigned a rank according to differential expression Pathways enriched in this list are identified and displayed as an visual map which organizes pathways by overarching themes
- Visualize · Pathway Guide
Our expanded cluster shows the constituent pathways that include our IL-5 gene set The edges indicate shared genes, but to get a better idea of the overlap, let’s look at the overlap in all pairs of gene sets in table format (Figure 14)
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