pathway analysis tools for xenopus
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8.0 years ago
mike ▴ 90

Hello,

I am working with xenopus laveis genome.Is there any pathways analysis tool (apart from KEGG) which takes multiomics data for xenopus laveis?

Thanks

pathways omics xenopus • 2.5k views
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Please state the reason to not consider KEGG bit clearer !! and also mention in detail what is your requirement for reference functional database (pathway database)?

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@EagleEye With KEGG I am getting only 10% of the genes from my dataset mapped to the pathways and same goes for metabolites. I am looking for a tool which can give me more genes and metabolite from my list in the pathway.

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Which tools did you try? Because it depends on how the tool is using the database resource, whether it is updated resource or the older version of KEGG.

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I am using KEGG Mapper. How can I check the version of KEGG Mapper on the interface? So far I haven't found any pathway tool which uses xenopus as a reference.

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Try GeneSCF, it is real-time based tool uses current KEGG directly from the source.

Gene Set Clustering based on Functional annotation (GeneSCF)

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I read the documentation for this tool.. seems promising. WIll it also handle metabolites in future?

I get the following error when I tired it

Illegal division by zero at /home/shh2026/Documents/geneSCF-master-source-v1.1/class/lib/List/Vectorize/lib/List.pl line 599, <in2> chunk 1.

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Right now it can handel only Entrez GeneID and Gene Symbols. If you get this error please have a look at this,

https://github.com/santhilalsubhash/geneSCF/issues/2

https://github.com/santhilalsubhash/geneSCF/issues?q=is%3Aissue+is%3Aclosed

If you still get the issue, please comment here.

We are currently working extensively on adding more features to GeneSCF, future version will be improved.

JFI: In your case you should use 'update' mode from GeneSCF because, GeneSCF download comes with only 'Human' database. The update mode will download the KEGG resource and do enrichment analysis.

./geneSCF -m=update -i=[INPUT FILE] -t=[gid|sym] -o=[OUTPUT PATH/FOLDER/] -db=KEGG -p=yes -bg=[#TotalBackgroundGenes] -org=xla

Sample input Gene Symbols for xla:

slc5a11

foxd3-a

cypxl301-a

t2

met

crb2

zbtb7b

sal-3-a

tbx4

tbx5-a

Sample input Entrez IDs for xla:

373547

373548

373549

373550

373551

373552

373553

373554

373555

373556

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I have already used -m=update option in command and xla folder is generated under db folder too. I also tested the example which is provided in the documentation and it is giving me same error.

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can you please enter the command used to run test dataset ?

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./geneSCF -m=update -i=/home/Desktop/GeneSCF/gene1.list -t=gid -db=KEGG -o=/home/Desktop/GeneSCF -org=xla --plot=yes --background=20000

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One more request, please also provide some lines of your input. Because this error usually means none of the input genes are matching with the KEGG database.

http://genescf.kandurilab.org/faqs.php

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379087 443741 380084 379924 380589 734364 444644 496247 446645 444262 735017 398353 380572 494639 378517 495080 379818 447106 379775 432055 380128 495369 446392 734304 394334 397913 379740

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I hope these are new line separated (one gene per line). And also please check the system requirement for GeneSCF,

System requirements: GeneSCF only works on Linux system, it has been successfully tested on Ubuntu, Mint and Cent OS. Other distributions of Linux might work as well. If something goes wrong, please test whether these commands are woking fine on your teminal, awk, cat, gzip, wget, rm, mkdir, sort, date, sed, paste, join, grep, curl, echo (Still it needs Linux to run successful)

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Hi Mike,

This solution might work, split GeneSCF run into to two steps,

1) Download updated resource for XLA from KEGG

./prepare_database -db=KEGG -org=xla

2) Run normal mode on downloaded data

./geneSCF -m=normal -i=/home/Desktop/GeneSCF/gene1.list -t=gid -db=KEGG -o=/home/Desktop/GeneSCF -org=xla --plot=yes --background=20000

Because I tested with the sample gene list you provided, it works without any problem on Linux (Ubuntu, Mint and CentOS).

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Thanks for your answer. The problem was with "line-ending" while saving the gene1.list file.

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