I've been dealing with gene-expression\gene-set analysis for about 6 years now, started with micro-arrays and recently RNAseq data, yet I still haven't found a convenient & reliable software to handle these tasks. I turn to you BioStars -perhaps you can point me at some neat tools I have been missing all these years? :)
The basic task I wish to conduct is to assess the statistical significance of changes to various custom gene-sets I input, clustering & graphical representation of the output is a nice bonus, but not a must.
These are some the tools I'm currently using:
Thanks for taking the time to read through, open to all suggestions.
Roy
edited:
P.S - please refer me to non-commercial software
•
written
by
roy.granit
Thanks, but I was thinking of non-commercial ones.
•
written
by
roy.granit
This is a good review:
"Methods and approaches in the topology-based analysis of biological pathways"
Why not a DIY solution in your preferred programming language?
•
written
by
Jean-Karim Heriche
I think that since so many people are doing this it would be better to build upon some well tested robust code.
•
written
by
roy.granit
R package, cogena, probably is one of your options. The custom gene-sets is accepted if formatted as gmt (so far, only gene symbol is supported due to the internal gene sets. but if your input genes and gene sets are all Entrez IDs, cogena should work.) Graphical representation of the output is also a feature of cogena. I do not know what's the meaning of clustering here, but cogena cluster DE genes and the do pathway analysis for the clustered genes as well as All the DE genes.
See post Drug repositioning based on co-expressed gene set enrichment analysis, cogena also.
Another tool is enrichr, though the custom gene set is not allowed so far.
Hope helpful.
•
written
by
Zhilong Jia
Thanks! as for cogea, looks cool - if I understand correctly it requires one to create some clusters and then preform the gene-set analysis, right? or can you skip the first step?
Cogena clusters genes internally. If you just want to do pathway analysis of all de genes, cogena shows the result always , together with pathway for clustered genes.
How about GeneSCF,
More reliable because it holds up-to-date information (also real-time features). Specifically designed to avoid using outdated databases/information.
User friendly (computation biologists)
No installation
Can be easily integrated with any pipeline
Support for all organisms covered by KEGG and gene ontology
Now that it's been >2.5 years maybe some has some cool software to recommend?
Log in to answer this question.
Sounds like you have additional constraints? GUI? Cross-platform? What databases included?
I'm using a Mac, but have access to a PC if needed. A nice GUI is a plus of course, but if you know a great package that can make this easy that's also OK. I'll be uploading my own gene-sets, so no specific DB is required (most of my sets are already in Entrez ID, so it would be nice to keep that).