Creating Go Chart Using Available Go Ids

Question

[Raghul]

Hi I have set of genes with GO IDs. I obtained this data using CAMERA workflow for "Metagenomic data annotation and clustering ". Now I want "to get a rough idea how these annotated sequences are distributed in different gene categories". For this aspect CateGOrizer was good but this tool gives information for all 3 categories in a single pie diagram. It will be better to have 3 different pie for each category. I tried REViGO but it dont give the visual representation for all available sequences but only few selected sequences. I have around 8000 sequences. can anybody please give me a suggestion to visualize the data as I want? You can see the data below!

thank you very much raghul

#query    GO    reference DB    reference family    e-value    description
contig00965.4    GO:0006412    TIGRFAM    TIGR00001    2e-29    translation 
contig00965.4    GO:0022625    TIGRFAM    TIGR00001    2e-29    cytosolic large ribosomal subunit 

contig00965.4    GO:0000315    TIGRFAM    TIGR00001    2e-29    organellar large ribosomal subunit 

contig00965.4    GO:0003735    TIGRFAM    TIGR00001    2e-29    structural constituent of ribosome 

contig37137.2    GO:0006412    TIGRFAM    TIGR00001    2e-21    translation 

contig37137.2    GO:0022625    TIGRFAM    TIGR00001    2e-21    cytosolic large ribosomal subunit 

contig37137.2    GO:0000315    TIGRFAM    TIGR00001    2e-21    organellar large ribosomal subunit 

contig37137.2    GO:0003735    TIGRFAM    TIGR00001    2e-21    structural constituent of ribosome 

contig00611.6    GO:0006412    TIGRFAM    TIGR00001    9.5e-20    translation 

contig00611.6    GO:0022625    TIGRFAM    TIGR00001    9.5e-20    cytosolic large ribosomal subunit 

contig00611.6    GO:0000315    TIGRFAM    TIGR00001    9.5e-20    organellar large ribosomal subunit

[Irsan]

So you want to make a pie-diagram where each piece of the pie is one of the unique GO-terms (GO:0006412, GO:0000315), the size of the splices corresponds to the amount of contigs in that GO-term, and then make such a pie-chart for each unique reference family? But in you example table, there is only 1 reference family so making one pie-chart seems logical here ...

[sarahhunter]

Or do you mean each GO category: Biochemical Process, Molecular Function and Subcellular categorization?

[Raghul]

I have shown here only few lines of data out of over 8000 lines. I just want to know the viewers to have an idea about the data I have. The 3 categories I mention is Biological process, Cellular component, Molecular function

Answer 1

[sarahhunter]

If you want to be able to summarise your metagenomics results in GO terms, it may be useful to use the metagenomics GO slim my team created together with Jane Lomax (Gene Ontology supremo) - the OBO formatted file is here: http://www.geneontology.org/GO_slims/goslim_metagenomics.obo

The slim allows you to focus in on terms that are at a suitable level of detail in the ontology (the idea being, if the terms are too specific, they'll get lost in the noise; if they're too general they're not really very useful)

We use the slim to summarise the outputs from the EBI metagenomics analysis pipeline and generate static bar charts for each of the GO categories. You can see an example at the bottom of this page: https://www.ebi.ac.uk/metagenomics/analysisStatsView/SRS086444

I know this isn't exactly what you were asking to do. But if you applied a slim to your results, you might be able to generate the view you want in (gasp!) Excel or something similar.

[Raghul]

OK, thank u! I got the concept you have explained! "We use the slim to summarise the outputs from the EBI metagenomics analysis pipeline and generate static bar charts for each of the GO categories" - So How to do this ? Does EBI metagenomics pipeline does this or I have to do it separately? thank you very much!

[sarahhunter]

The metagenomics pipeline does this slimming but we can probably help you to do the same on your data set (just contact the team using http://www.ebi.ac.uk/support/metagenomics).

Regarding visualisation, we're currently looking at using Krona (http://sourceforge.net/p/krona/home/krona/) for these data, however, we haven't yet figured out how to do this sensibly with the full multi-level GO, only the slim. There are detailed instructions about how you can use Krona to view data in (e.g.) Excel on the Krona page linked above.

Answer 2

[lzsph]

Maybe you should use blast2go, but you may have to format your data shown above into the .annot format required by blast2go and import it to b2g. Command Or Script To Generate An Annotation File For Blast2Go

[Raghul]

The data shown cannot be formatted but it is possible to upload the proteins & do GO by blast2go. I was wondering before using blast2go because it is designed to analyse non-model organisms & I have bacterial data! Anyway I am trying both ways suggested & look into the results!