Pathway Enrichment Analysis

The Component uses IDs from several data sources to create an interactive pathway analysis based on the web service of Reactome.
The input for the pathway enrichment analysis can either be a column that can be selected from the input table or IDs that can be inserted directly in the component configuration.
If you use an input column and additionally paste IDs in the cofiguration window, the two input columns will be concatenated.

Allowed identifier types are for example:

UniProt identifiers: P30304
ChEBI identifiers: 15422
COMPOUND identifiers: C00002
Gene Ontology (GO) acession numbers: GO:0030060
Enzyme Classification (EC) numbers: 1.1.1.37
NCBI Gene: 4171
Protein Data Bank (PDB) identifiers: 1cbs
Ensembl identifiers: ENSG00000141736

For more information about available identifiers visit:

https://reactome.org/linking-to-us


In the final view it is possible to select pathways in the bar chart and have it displayed in a table view. The selected pathways, associated genes, IDs and p-values will then serve as output for the component. If nothing is selected all found results will serve as output.


For more infos about Reactome visit:

https://reactome.org/
https://www.ncbi.nlm.nih.gov/pubmed/28249561
https://www.ncbi.nlm.nih.gov/pubmed/29145629

Options

Select the column containing valid IDs.

The column should contain valid IDs for the pathway analysis.

Select the number of pathways shown in the bar chart.

To make the labels on the bar chart easier to read, the number of displayed pathways can be selected here. The pathways are taken from the top of the table and are therefore the most relevant.

Enter list of IDs

Enter valid IDs for pathway analysis as written in the component description.

Nodes

• Column Filter5 ×
• Table Row to Variable5 ×
• GroupBy4 ×
• JSON Path4 ×
• Rule Engine4 ×
• Show all 28 nodes

Extensions

• FeatureKNIME Base nodes
• FeatureKNIME JavaScript Views
• FeatureKNIME Javasnippet
• FeatureKNIME JSON-Processing
• FeatureKNIME Math Expression (JEP)
• Show all 7 modules

Links

• No links available