Gene ontology enrichment analysis tool

[rozitaa]

Hi All,

I am working with microarray data. I have some genes of interest that I want to know the GO enriched terms. So far I have found them by GOstat. I also want to know if the representing GO is down/up regulated. Or at least which genes are involving in the representing GO then I can figure it out my self. Do you know any tools that provide me with this?

Thanks

[GenoMax]

Have you looked at DAVID: http://david.abcc.ncifcrf.gov/

Also GenePattern: http://www.broadinstitute.org/cancer...esc/expression

[rozitaa]

Yes I have seen david but that one only clusters genes and not Gene ontologies.

[bigmw]

You may try GAGE if you know R. It works with both microarray and RNA-Seq data.

http://bioconductor.org/packages/release/bioc/html/gage.html

http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/gage.pdf

[evanharrell]

I am trying to use gage to do a go term analysis on drosophila RNA-seq data.

All of the vignettes tell very nicely how to find kegg pathway gene sets for different species to do the analysis with but is there a way to get simple go terms for drosophila? I have downloaded the flybase go terms (.fb file) and it seems to be in a very different format than the go.sets.hs and go.subs.hs sets in the vignettes. Is there an easy way to convert these go terms to the appropriate format?

[wetSEQer]

You may try GAGE if you know R. It works with both microarray and RNA-Seq data.

http://bioconductor.org/packages/release/bioc/html/gage.html

http://bioconductor.org/packages/rel...t/doc/gage.pdf

What is the difference between Heatplus and GAGE? Do you know? I just began to search a tool to do my work and I saw your reply and wonder you might know which one is better.

[bigmw]

Bioconductor has two annotation data packages: org.Dm.eg.db and GO.db. You may use these two packages to generate the GO gene sets for fly. In other words, you can extract GO term IDs from GO.db, and map the GO terms to Entrez Gene ID using org.Dm.eg.db. Hope this is clear enough.

I am trying to use gage to do a go term analysis on drosophila RNA-seq data.

All of the vignettes tell very nicely how to find kegg pathway gene sets for different species to do the analysis with but is there a way to get simple go terms for drosophila? I have downloaded the flybase go terms (.fb file) and it seems to be in a very different format than the go.sets.hs and go.subs.hs sets in the vignettes. Is there an easy way to convert these go terms to the appropriate format?

[bigmw]

Gage is a tool for gene set, GO and pathway analysis, it provide functions to visualize the analysi results, like heatmap and scatterplot. Heatplus is a tool dedicated to heatmap plotting. They are not really the same type of tools.
For more details on gage:

http://bioconductor.org/packages/release/bioc/html/gage.html

What is the difference between Heatplus and GAGE? Do you know? I just began to search a tool to do my work and I saw your reply and wonder you might know which one is better.

[ygc_hku]

You may interesting in using clusterProfiler package: http://www.bioconductor.org/packages...rProfiler.html

[rozitaa]

You may interesting in using clusterProfiler package: http://www.bioconductor.org/packages...rProfiler.html

Thanks seems so interesting I will look into it.

[angel-sakura]

Hi, I'm currently using clusterProfiler for GO enrichment analysis. It is a great tool but I have encountered a problem of inputing data. I read through the manual and find nothing about how to input my own data or what is the format of input data. Could you please shed light on it?
Thank you very much!
Y

[ygc_hku]

Hi, I'm currently using clusterProfiler for GO enrichment analysis. It is a great tool but I have encountered a problem of inputing data. I read through the manual and find nothing about how to input my own data or what is the format of input data. Could you please shed light on it?
Thank you very much!
Y

The input of enrichGO is a vector of entrez gene ID. The manual do explain this.

[angel-sakura]

Sorry about my carelessness, I just focused on the scripts when I read the manual.
From the example data(geneList), geneList seems to contain two values, one is entrez Id, what about the other one? Is it P-value? If so, does P-value come from the cuffdiff DE results?

Thank you!

[ygc_hku]

Sorry about my carelessness, I just focused on the scripts when I read the manual.
From the example data(geneList), geneList seems to contain two values, one is entrez Id, what about the other one? Is it P-value? If so, does P-value come from the cuffdiff DE results?

Thank you!

The value is fold change, it can be p-value.

The values were used in gene set enrichment analysis for ranking the genes.

But for hypergeometric test, only entrez gene IDs are needed.

[angel-sakura]

The value is fold change, it can be p-value.

The values were used in gene set enrichment analysis for ranking the genes.

But for hypergeometric test, only entrez gene IDs are needed.

Thank you ! Now I get it working.

Cheers