Question: The quest for the perfect gene-set analysis software
1
gravatar for roy.granit
3.3 years ago by
roy.granit740
Israel/LabWorm
roy.granit740 wrote:

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:

# Genomica - Good old Genomica is piece of software, and does the job very nicely with hyper-geometric distribution! the only trouble is that's it's really outdated, and has lot's memory issues which makes it really hard to load large amount of data. Also, one cannot just copy-paste genesets, but have to go thought some laborious work to format the sets. 

#  GSEA - On first sight it looks like a winner, but I find it almost impossible to get it to run properly, and I simply hate formatting the input data (and the whole java interface). 

# Expander - Seems promising, but not that intuitive to use (I was not able to download the most recent version). 

Thanks for taking the time to read through, open to all suggestions.

Roy

 

edited: 

P.S - please refer me to non-commercial software

tool analysis software geneset • 1.1k views
ADD COMMENTlink modified 10 months ago by EagleEye5.8k • written 3.3 years ago by roy.granit740
1

Sounds like you have additional constraints?  GUI?  Cross-platform?  What databases included?

ADD REPLYlink written 3.3 years ago by Sean Davis25k

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).

ADD REPLYlink written 3.3 years ago by roy.granit740
2
gravatar for Woa
3.3 years ago by
Woa2.7k
United States
Woa2.7k wrote:

http://www.advaitabio.com/ipathwayguide.html#page=page-1

ADD COMMENTlink written 3.3 years ago by Woa2.7k

Thanks, but I was thinking of non-commercial ones..  

ADD REPLYlink written 3.3 years ago by roy.granit740
2
gravatar for Woa
3.3 years ago by
Woa2.7k
United States
Woa2.7k wrote:

This is a good review:

"Methods and approaches in the topology-based analysis of biological pathways"


http://journal.frontiersin.org/article/10.3389/fphys.2013.00278/abstract

ADD COMMENTlink written 3.3 years ago by Woa2.7k
1
gravatar for Jean-Karim Heriche
3.3 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche16k wrote:

Why not a DIY solution in your preferred programming language ?

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Jean-Karim Heriche16k

I think that since so many people are doing this it would be better to build upon some well tested robust code. 

ADD REPLYlink written 3.3 years ago by roy.granit740
1
gravatar for Zhilong Jia
3.3 years ago by
Zhilong Jia1.4k
London
Zhilong Jia1.4k wrote:

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 Co-expressed gene set enrichment analysis, cogena also.

Another tool is enrichr, though the custom gene set is not allowed so far.

Hope helpful.

ADD COMMENTlink written 3.3 years ago by Zhilong Jia1.4k

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?

ADD REPLYlink written 3.3 years ago by roy.granit740

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.

ADD REPLYlink written 3.3 years ago by Zhilong Jia1.4k
1
gravatar for EagleEye
10 months ago by
EagleEye5.8k
Sweden
EagleEye5.8k wrote:

How about GeneSCF,

  1. More reliable because it holds up-to-date information (also real-time features). Specifically designed to avoid using outdated databases/information.

  2. User friendly (computation biologists)

  3. No installation

  4. Can be easily integrated with any pipeline

  5. Support for all organisms covered by KEGG and gene ontology

ADD COMMENTlink written 10 months ago by EagleEye5.8k
0
gravatar for roy.granit
10 months ago by
roy.granit740
Israel/LabWorm
roy.granit740 wrote:

Now that it's been >2.5 years maybe some has some cool software to recommend?

ADD COMMENTlink written 10 months ago by roy.granit740
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1941 users visited in the last hour