{% extends "base.html" %} {% import "bootstrap/wtf.html" as wtf %} {% import "bootstrap/fixes.html" as fixes %} {% import "bootstrap/utils.html" as util %} {% block title %}Enriched Pathways{% endblock %}xz {% block styles %} {{ super() }} {% endblock %} {% block scripts %} {{ super() }} {% include "dependencies/datatables.html" %} {% endblock %} {% block content %}
The enriched pathways are presented in different tables for each resource loaded into ComPath. Each table links the pathway info page where the genes in the pathway that has been submitted will be highlighted. Furthermore, this page presents you the curated mappings with similar pathways. The second column will open the pathway page in the original pathway database. The pathway enrichment is presented in the third column (adjusted p-values) by performing a Fisher's Exact Test for each mapped pathway in all resources and adjusting the p-values for multiple testing using Benjamini & Hochberg correction (rounded to 4 decimal places). The adjusted p-values (q-values) measures in a certain degree how enriched is pathway is as a way of filtering pathways for further analysis.
Gene Symbols Submitted ({{ submitted_gene_set|length }}) | {% for hgnc_symbol in submitted_gene_set %} {{ hgnc_symbol }} {{ "," if not loop.last }} {% endfor %} |
Genes not in any pathway ({{ genes_not_in_pathways|length }}) | {% for hgnc_symbol in genes_not_in_pathways %} {{ hgnc_symbol }} {{ "," if not loop.last }} {% endfor %} |
Number of Pathways Mapped | {{ number_of_pathways }} |
Select All Pathways |
First, select your pathways of interest and then, choose the type of analysis to perform. The "Overlap View" displays the boundaries between the selected pathways represented as Venn or Euler diagrams. The "Cluster View" renders an interactive dendrogram of the pathways clustered based on their distances. Finally, the "Network View" displays the knowledge around the selected pathways as well as the similarity between them enabling to identify interplays.
Pathway Name | Resource Identifier | Adjusted p-value | Genes Mapped | Pathway Size | |
---|---|---|---|---|---|
{{ enriched_pathway["pathway_name"] }} | {% if resource_name == "reactome" %} {{ enriched_pathway["pathway_id"] }} {% elif resource_name == "kegg" %} {{ enriched_pathway["pathway_id"] }} {% elif resource_name == "wikipathways" %} {{ enriched_pathway["pathway_id"] }} {% elif resource_name == "msig" %} {{ enriched_pathway["pathway_id"] }} {% else %} {{ enriched_pathway["pathway_id"] }} {% endif %} | {{ enriched_pathway["q_value"] }} | {{ enriched_pathway["mapped_proteins"] }} | {{ enriched_pathway["pathway_size"] }} |