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1. Can I do pathway analysis using R?
(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 ...
2. Can I submit a list of differentially expressed genes, as log2 fold change values, coming from two different conditions to have a quantitative representation of pathways involvement?
(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 ...
3. Can I submit a list of differentially expressed genes, as log2 fold change values, coming from two different conditions to have a quantitative representation of pathways involvement? If yes, how can I ...
(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 ...
4. Chemical coverage of human biological pathways
(Spotlight)
In the feature article of the October 2024 issue of Drug Discovery Today titled “Chemical coverage of human biological pathways”, Kwak et al. describe the Target 2035 initiative, whose mission is to discover ...
5. Circadian transcriptional pathway atlas highlights a proteasome switch in intermittent fasting
(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. ...
6. Common targetable inflammatory pathways in brain transcriptome of autism spectrum disorders and Tourette syndrome
(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 ...
7. Contribute Pathway Knowledge
(Community)
Become a Reactome contributor! You will be credited with authorship or reviewership for all of your contributions. Each pathway is associated with a DOI and can be cited as a publication. You can quickly ...
8. COVID-19 Disease Pathways
(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 fast-tracked ...
9. COVID-19: SARS-CoV-2 infection pathway Released
(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 ...
10. Does Reactome contain pathway information from non-human species?
(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 ...
11. Download our biological pathway knowledge in a PDF book
(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 ...
12. Gene set enrichment analysis (GSEA) identifies upregulated carbohydrate metabolism pathways in tumors with high tumor-specific total mRNA expression (TmS)
(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 ...
13. How can I find all pathways reported for one organ? For example, I want to extract all reported pathways in (tissue X) for (species Y).
(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 ...
14. How can I use Neo4J to identify all the genes for a given pathway?
(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) ...
15. I have a list of input genes. I want to retrieve all the pathways in which the genes are involved. How can I do this using a Neo4j Cypher query?
(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) ...
16. I have a list of Reactome pathway IDs. I want to find whether any of them are disease pathways and also retrieve associated disease names. Is it possible to retrieve the information using API or neo4j ...
(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 ...
17. I have a proteomics data set that I would like to use for quantitative pathway analysis. Is there training material available to help me?
(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 ...
18. I used the “Analyse gene expression” tool with my mouse proteomics data set. I notice that the database is based on human pathways – does the software automatically convert my mouse gene names to the human ...
(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 ...
20. Is it possible to know how many of my uploaded genes are found within each specific hierarchical pathway category identified in the Reacfoam view? For instance, how many of my genes belong to pathways ...
(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 ...
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