gene functional analysis using GO and KO numbers
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6.4 years ago

dear all, im interested to find out the functional analysis of my genes (biological process, cellular component and molecular function etc). I do have GO and KO annotations of my gene but could not find out any good software that could give me functional analysis along with graphical representation. kindly suggest me any software that either could use GO and KO information or simply fasta protein formate to functionaly characterized besides BlastQuala that im already using. thanks
rna-seq • 4.8k views
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I am sorry but this question is not clear to me, I do have GO and KO annotations of my gene but could not find out any good software that could give me functional analysis along with graphical representation?

In my opinion, if you have KO and GO ids for your genes then you can easily represent it with the help of excel or R. Lets say bar graph/pie chart for 10 most abundant KOs or pie donut for top 10 GOs etc.

You can use WEGO for GO representation.

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sorry for the inconvenience. let me re-explain the question. I have gene ontology (GO IDs) and KEGG pathway (KO annotations both for homology and pathway description). im unable to use these file in GO website to characterize then functionally as this site needs to select pre_listed genome where my genome is not there. im interested to classify them in biological cell compartment and funtion numericaly and graphicaly which is not possible just by looking at the GO IDs. looking for the software that could help to do so. hope have elaborated the question.kind help will highly be appreciated.

my KOmy look like this

tton_A_25961_BGI-A2_v1.0    K01256
Cotton_A_25965_BGI-A2_v1.0  K09872
Cotton_A_25973_BGI-A2_v1.0  K07375
Cotton_A_20183_BGI-A2_v1.0  K02949
Cotton_A_25963_BGI-A2_v1.0  K20717
Cotton_A_32011_BGI-A2_v1.0  K02872

while GO file as :

Cotton_A_00026_BGI-A2_v1.0   GO0005216|GO:0055085
Cotton_A_00026_BGI-A2_v1.0   GO0005247|GO:0006821|GO:0016020
Cotton_A_00026_BGI-A2_v1.0   GO0005247|GO:0006821|GO:0016020|GO:0055085
Cotton_A_00026_BGI-A2_v1.0   GO0030554
Cotton_A_00028_BGI-A2_v1.0   GO0003824|GO:0008152

thanks

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Thanks for your re-explanation.

In this case I think you have to take look on QuickGO, bioDBnet or amigo goose API.

I am not sure about batch search in QuickGO but some RESTFull API is there to access GO descriptions using GO ids. In the case of bioDBnet we can do a batch search by using both KEGG as well as GO Ids. Amigo GOOSE is a web-based API (We can design MySQL query) for accessing GO descriptions using GO IDs.

And one more advice you have to polish you GO IDs because in some ids colon (:), is missing so your IDs should be GO:0005216, GO:0005247, GO:0030554 and GO:0003824

you can also use KEGG static URL with your KEGG ID.

Have a look on this Example for K01256.

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im sorry that im troubling you again but im pretty much confused about the outputs of these programs. let me share one by one: 1) the program like WEGO is something that im looking for but unfortunately its not working and im getting following message while uploading even their demo file : <html> <head><title>502 Bad Gateway</title></head> <body bgcolor="white">

502 Bad Gateway

The proxy server received an invalid response from an upstream server. Sorry for the inconvenience.
Please report this message and include the following information to us.
Thank you very much!

URL: http://wego.genomics.org.cn:50028/file/upload
Server: r276b9178.cloud.am55
Date: 2018/07/07 18:20:56
</body> </html> while even there contact mail is not responding,

2) for quick go i get something like this (that could solve my problem) for which there is no export option rather it give output only will all the annotated gene in other species that are useless for me. Your Selection:6 terms Biological Process (3) GO:0008610 lipid biosynthetic process
GO:0000002 mitochondrial genome maintenance
GO:0000003 reproduction
Cellular Component (1) GO:0000139 Golgi membrane
Molecular Function (2) GO:0046872 metal ion binding
GO:0005515 protein binding

3) and ammigo is accepting only one entry not batch selection. im newbie to bioinformatics and i could not understand the Amigo GOOSE web-based API

4) bioDBnet is also working poorly. once it work it simply gives list of hierarchy of homolog GO and their function but i could not understand that what spesific function out od this list should i assign to my gene???

need your further help

thanks

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for WEGO, I would suggest just clear your browser cache/history and see it is working or not.

for QuickGO use this API. Here you just have to put comma separated list of GO Ids and you can download results in JSON format, further you can use any JSON to text converter and you will get the TSV file (OR if you can write small JSON parsing script then it would be better, you can customize the output by your own).

for AmiGO GOOSE API use the below query and search. While searching just click on Download results directly in a text format checkbox. Replace these IDs with your original ids and see if it working or not.

SELECT * FROM term WHERE acc IN ('GO:0005634','GO:00086','GO:0000003','GO:0000139','GO:0046872','GO:0005515');
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Dear nitinnarwade thank you so much for all your kind help and precious time to help me out. as per your suggestion AmiGO GOOSE is giving nice output in the form i need. can you please help me out to resolve one more issue??. In many articles i have found sub categorization of 3 broad categories: celluar, molecular and biological e.g for biological process there are sub categories of metabolism, cell cycle, cell process, catabolic etc etc. I have tried to look into GO ontology files for sub categories available at http://geneontology.org/page/download-ontology and also in many softwares (backup files) so that i could sub categorize my GO IDs but in vain. is there any key , software available for it??? or do you help me how to resolve it??? i want to draw graph like WEGO manualy as WEGO is totaly non functional despite f removing all catche.

thanks in anticipation

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I would prefer pie donut for Gene Ontology representation. I have used highchart pie donut javascript (Customized) for such representation.

chart

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+1 for that Nitin. I would love to explore that!

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nitinnarwade1504 : How to add images to a Biostars post

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this is an excellent way of representation. many many thanks for the tool. you ve brought a bbiggner like me out of this juggling stat step by step for which i really appreciate your efforts.

but my question was that is there ant key to sub categorize GO terms under 3 basic categories like i gave the example of biological process there are sub categories of metabolism, cell cycle, cell process, catabolic etc etc. ????

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Hello blooming.daisy333

You should up-vote or accept an answer if that helped. This not only encourages the person helping you but also help other people looking for solutions to similar problems.

enter image description here

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dear vijay im already upvoting. infact all these answers of nitinnarwade are to the point and realy very helpful. many thanks to him/her.

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