Question: gene ontology visualisation
0
gravatar for gaughey
2.3 years ago by
gaughey10
gaughey10 wrote:

Hi

Does anyone know how to make a GO enrichment diagram like the one in fig 1D of this paper? http://www.sciencedirect.com/science/article/pii/S2211124715006075

Unfortunatley they don't say how the figure was constructed. I've seen a few tools for this, like revigo (http://revigo.irb.hr/) which is ok, but normally ends up with a big mess of confusing bubbles. Ideally I'd like to show all three ontologies (MF, CC + BP) in the same diagram like in the example, but this isnt a feature of any tools that I'm aware of.

If anyone knows what was used to make this figure, or of any other tools that can do this, I would be grateful to hear from you.

Thanks!

rna-seq chip-seq gene • 1.4k views
ADD COMMENTlink modified 2.2 years ago by EagleEye6.3k • written 2.3 years ago by gaughey10
2

Unfortunately their methods are not well described, which makes it not transparent (I would say the reviewers did a lousy job).

They don't even mention which GO analysis tool they used (there are 100s of different tools!!).

The figure itself looks like it was made with Rgraphiz, maybe you should check that out.

ADD REPLYlink written 2.3 years ago by Benn6.8k

Great, thanks! I'll have a go with Rgraphviz and see what I can come up with.

ADD REPLYlink written 2.3 years ago by gaughey10

Maybe first do the go analysis with goseq?

ADD REPLYlink written 2.3 years ago by Benn6.8k

I don't know how they did it. But there is a good chance that there is no tool that shows you these things right away nicely but that they did some manual editing to get there and that is ok as well. You don't want 'only' the structure but also size/colours based on pValue, right?

ANYWAY - please don't talk about three ontologies. You got me confused there because you are wrong. You talk about the Gene Ontology not about three different ontologies (Because that would be a whole different 'problem')

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by LLTommy1.2k
1

Why are they wrong? If, in their experience, all software handles BP, MF and CC separately and they want it all together then that is a problem they need to overcome.

ADD REPLYlink written 2.3 years ago by Emily_Ensembl18k

Because it is the Gene Ontology, it is one ontology. You are not comparing different ontologies. So to label this a problem of 'comparing three different ontologies' is wrong.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by LLTommy1.2k
2

They didn't talk about "comparing different ontologies". I think your response is quite facetious and unnecessary.

ADD REPLYlink written 2.3 years ago by Emily_Ensembl18k

Apologies, all I point out is that it's one ontology not three. And yes, he posts:

I'd like to show all three ontologies

which led me to explain that it's not three ontologies but one. I don't know why that bothers you. And yes it makes a difference. If you say you want to show 'all three ontologies (BP, MF, CC)' - then I am thinking, why does he want to compare the 'Mental Functioning Ontology' (abbreviation=MF) now with the gene ontology? And which ontology is CC, does he talk about the Cell Cycle Ontology? So I posted that this got me confused for a second and led to me saying that GO is one ontology, not three.

But before you call my post facetious and unnecessary then think about what you actually did contribute to this thread.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by LLTommy1.2k
1

Can you please start a new thread (forum) if the misuse of the name ontology bothers you?

I think most people will understand the question, and ontology is used more often to indicate MF, CC or BP. For example, goseq results output gives a column named 'ontology'.

ADD REPLYlink written 2.3 years ago by Benn6.8k

Thanks for your comments all. Apologies if I caused any confusion. Clearly, I don't know a lot about gene ontology (which is why I am here asking questions...). To clarify: In my experience GO analysis tools normally yield three seperate ontological descriptors, (BP - biological process, CC - cellular compartment, and MF - molecular function), which I have (perhaps incorrectly) referred to as "ontologies". These three seperate components have been represnted as seperate branches of a network diagram in the figure I linked to. I was dissatisfied with the available tools which would only represent these three components seperately, as I thought it more appropriate to display a more holistic GO enrichment diagram. Ironically, this seems to be largely in agreement with the point that LLTommy is making. LLTommy - I'm sorry to say that your comment did come across as a little rude, but I appreciate that you are trying to help, and it is very difficult to convey intent on these kinds of forums. Perhaps you could let us know how you would define these subcategories to avoid future confusion? Then we can move away from semantics and back to bioinformatics, which is what we are here for! :)

ADD REPLYlink written 2.3 years ago by gaughey10

Perhaps "classes" would have been more apt. https://en.wikipedia.org/wiki/Ontology_components

ADD REPLYlink written 2.3 years ago by gaughey10

Hi gaughey. I am sorry that my comment came across as rude and I can see why, apologies for that - I just typed the answer inbetween a lot of other stuff. In no way I mean that your question is not valid or that your problem is not correct, I just wanted to point out that your work with one ontology, not many. SO instead of saying 'you were wrong' all I wanted to say, it is wrong to call these 3 different ontologies. So apologies, I know that my answer sounded rude, it was not meant to be. And it is not that big of a deal neigther, but I just feel like if you don't point out a false statement like that, how could people learn. And yes, you are on point, the three things are classes and obviously 'top level' - however, they are all part the gene ontology, which is one ontology. Again, that is no big deal for your problem whatever, just a small little detail I wanted to make you aware of.

ADD REPLYlink written 2.2 years ago by LLTommy1.2k

I am sorry that my comment came across as rude and I can see why, apologies for that - I just typed the answer inbetween a lot of other stuff.

I appreciate that you answer questions "in between a lot of other stuff", but as you see here that didn't really lead to optimal results and was more a waste of energy for you and other responders. So perhaps it would have been better to delay your answer to when you had the time to properly make your point, albeit offtopic to this thread. I often add threads to my to do list for looking into those later.

Finally, written communication is tough. It's perfectly possible that you didn't want to be rude, but your intention is irrelevant. It's how it came across that does count.

ADD REPLYlink written 2.2 years ago by WouterDeCoster39k
1
gravatar for EagleEye
2.2 years ago by
EagleEye6.3k
Sweden
EagleEye6.3k wrote:

Hi, GeneSCF will provide you with similar results without any interaction ( as a bubble plot with number of genes in the term corresponding to size of the node and log10pvalue corresponding to y-axis) but for individual Gene Ontology category. Check the figures from the GeneSCF article for reference.

To avoid the mess, you can also select the process from the GeneSCF output to visualize (GOTERM<tab>no. of genes<tab>P-values) and use it as input to bubble.R script from GeneSCF source (genescf/class/scripts)

bubble.R output_selected_process.tsv output_path_folder organism_code database

GeneSCF is more flexible, you can play with it :-p

Other options...

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by EagleEye6.3k
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