Hello everyone. We have the list of differentially expressed genes. And we should check the pathways, that can be activated. Usually we use KEGG Pathways sources, but mb we can use something else? Thank you colleagues.
Hi Airat,
You didn't mention the organism. Besides Msigdb, as mentioned by Jochen, Reactome pathways (https://reactome.org/) is a good resource if it's human. You could also check out enrichments with PANTHER (http://www.pantherdb.org/) and DAVID (https://david.ncifcrf.gov/) which cover a larger range of organisms and other Gene ontology and Molecular function databases.
Hi Airat,
Here is another software:
STRING: functional protein association network
https://string-db.org/
Best,
Hediye.
Hi, you can use EnrichR as well:
https://maayanlab.cloud/Enrichr/
But simple enrichment should be meant for guidance only, you should go for the GSEA (gene set enrichment analysis) where the whole list of genes is sorted by some criteria (log2FC or p-value or FDR) used to decide what pathways are being enriched. This is better. You need to login, but it is free.
https://www.gsea-msigdb.org/gsea/msigdb/index.jsp
You can even use SPIA (signaling pathway impact analysis) to get an idea if the pathway is being activated or inhibited. It can be accessed using R software. There are variants of this method (fSPIA, I think) you can review the literature.
I came across another better option:
http://www.webgestalt.org/
for limited organisms, it can perform multiple tasks.
Good luck.
Hi Airat,
you csn use MetaCyc (https://metacyc.org/). It contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes.
Hello!
You can also check out the Flame online tool (http://flame.pavlopouloslab.info/) which runs functional enrichment analysis for you using 4 tools (aGOtool, gprofiler, WebGestalt and Enrichr) and can return enriched biological pathways from KEGG, Reactome, WikiPathways and PANTHER.
Just paste your gene list and select your organism of preference!
DAVID Functional Annotation Bioinformatics Microarray Analysis (ncifcrf.gov) and (17) (PDF) Pathway Marker Identification Using Gene Expression Data Analysis: A Particle Swarm Optimisation Approach (researchgate.net)(Pathway Marker Identification Using Gene Expression Data Analysis: A Particle Swarm Optimisation Approach | SpringerLink)@Airat Bilyalov
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