Use this tool to search the Reactome static web pages (Documentation, news, etc).
(API and R)
Although we don't provide a specific R package suitable for visualizing expression values on Reactome pathways, we do provide a full BioConductor package for quantitative pathway analysis based on expression ...
(FIViz)
If you want to use your log fold change data directly, you may use the Reactome Cytoscape app, described here (search for “Perform GSEA analysis”). This feature will sort your genes based on log fold change ...
(Reactome GSA)
... this feature are described here.
The Reactome GSA tool is an enhancement of GSEA and can take your original expression data directly, perform differential expression analysis and then highlight pathways ...
(Spotlight)
Reactome pathway gene sets in the MSigDB facilitated identification of the liver proteasome transcriptional switch that acts as the fasting timer in intermittent fasting in work published by Wei et al. ...
(Spotlight)
Reactome overrepresentation analyses of differentially expressed genes common to both Autism Spectrum Disorder and Tourette Syndrome help identify common targetable inflammatory pathways as described by ...
(Content)
Rapid and Precise Molecular Pathway Modeling of the SARS-CoV-1 and SARS-CoV-2 Infection Cycle with Human Host Protein and Therapeutic Interactions
In response to the COVID-19 pandemic, Reactome is fast-tracking ...
(News)
New Feature. In response to the COVID-19 pandemic, Reactome is fast-tracking the annotation of Human Coronavirus infection pathways in collaboration with the COVID-19 Disease Map group. Reactome release ...
(General website)
Reactome is centered on the molecular functions of human proteins. When possible, we annotate these functions with published evidence from work with human systems. When such evidence isn’t available, but ...
(News)
Aiming to make our biological pathway knowledge more accessible, we've been offering for years the option to download the complete content of our knowledgebase as a PDF book. Following users feedback ...
(Spotlight)
Gene set enrichment analysis (GSEA) conducted on Reactome’s carbohydrate metabolism pathways identifies the Pentose phosphate pathway and the Glucose metabolism pathway as the two most frequently upregulated ...
(General website)
... tool (select "Microarray data" for an example).
You can also use the "Tissue Distribution" tool to see how data from the Human Protein Atlas maps to Reactome pathway space.
Documentation is at ...
(Graph Database and cypher query)
... for a given pathway is
MATCH (n:DatabaseObject)-[:hasEvent|input|output|catalystActivity|physicalEntity|entityFunctionalStatus|diseaseEntity|regulatedBy|regulator|hasComponent|hasMember|hasCandidate|repeatedUnit|referenceEntity*]->(m:ReferenceGeneProduct) ...
(Graph Database and cypher query)
... Cypher query here.
To retrieve all human pathways for a single gene (for example: P36897, the Uniprot identifier for TGFR1)
MATCH (n)-[:referenceDatabase]->(rd:ReferenceDatabase)
WHERE toLower(rd.displayName) ...
(Graph Database and cypher query)
... with your pathway identifiers to the endpoint described here:
To know if a Pathway is a disease, look at the “isInDisease” property. The disease name is contained in the displayName of the diseases ...
(Reactome GSA)
To process quantitative proteomics data, the best, but also most complex analysis option is ReactomeGSA. A description of the tool, its use, and documentation are all part of this publication
There is ...
(General)
... GSA performs quantitative pathway analyses, increasing the statistical power of the differential gene expression analysis. The analysis software automatically converts the mouse proteins from your proteomics ...
(General website)
Unfortunately, this is not possible at this time.
(General)
At the moment we don’t have a way to filter the results by top level pathway, or diagram-level pathway or other criteria. This feature is on our radar to implement.
In the meantime, you can get a sense ...
(General website)
... documented here, and then added links to the Reactome pathways below a certain p value cutoff.
You could use that method to identify Reactome pathways that are related to a given KEGG pathway, and ...
(API and R)
Pathway analysis can be performed through our API, documented here.
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