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Question: retrieving pathways belong to my gene names
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Hi there!

Sorry guys, if my question has repeated before, I don't want waste your time, but I couldn't find proper answer for my question.

I am working with numbers of genes, I want to know to which pathway of KEGG database they belong? Indeed, I have written a program by python, using bioservices module, but there isn't any way to search several pathway in a run.how can I solve it by python? if anyone could help me, I appreciate it.

ADD COMMENTlink 19 months ago EFN • 0
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use kEGG rest api and post some example gene symbols

ADD REPLYlink 20 months ago
cpad0112
11k
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it is time-consuming way I think, need a faster way

can you help me?

ADD REPLYlink 20 months ago
EFN
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post some example gene symbols

ADD REPLYlink 20 months ago
cpad0112
11k
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some of my genes are : CRK, RUNX1, PSMD11,JUP , .......

Thanks

ADD REPLYlink 20 months ago
EFN
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It is unclear what exactly you have done so far. It sounds like you may have written a python program (that uses KEGG API?, since you used those tags) to do the search you need but you just want it done for several pathways. You may have to do some kind of a loop in that case but be aware that rapid programmatic querying may result in a IP ban from KEGG. You are supposed to buy a license (even for academic users) for extensive KEGG use.

ADD REPLYlink 20 months ago
genomax
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thanks for your response! No, I used bioservices module, I want to know if anyone can help me using API. maybe using loops is good idea.

ADD REPLYlink 20 months ago
EFN
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Format the output as per your needs:

> from bioservices.kegg import KEGG
> k = KEGG()
> genes=["CRK","RUNX1","PSMD11","JUP"]
> for i in genes:
        j=k.get_pathway_by_gene(i,"hsa")
        for keys,values in j.items():
            print(i,keys, values, sep="\t")

output:

CRK hsa04010    MAPK signaling pathway
CRK hsa04012    ErbB signaling pathway
CRK hsa04015    Rap1 signaling pathway
CRK hsa04062    Chemokine signaling pathway
CRK hsa04510    Focal adhesion
CRK hsa04666    Fc gamma R-mediated phagocytosis
CRK hsa04722    Neurotrophin signaling pathway
CRK hsa04810    Regulation of actin cytoskeleton
CRK hsa04910    Insulin signaling pathway
CRK hsa05100    Bacterial invasion of epithelial cells
CRK hsa05131    Shigellosis
CRK hsa05200    Pathways in cancer
CRK hsa05206    MicroRNAs in cancer
CRK hsa05211    Renal cell carcinoma
CRK hsa05220    Chronic myeloid leukemia
RUNX1   hsa04530    Tight junction
RUNX1   hsa04659    Th17 cell differentiation
RUNX1   hsa05200    Pathways in cancer
RUNX1   hsa05202    Transcriptional misregulation in cancer
RUNX1   hsa05220    Chronic myeloid leukemia
RUNX1   hsa05221    Acute myeloid leukemia
PSMD11  hsa03050    Proteasome
PSMD11  hsa05169    Epstein-Barr virus infection
JUP hsa05200    Pathways in cancer
JUP hsa05202    Transcriptional misregulation in cancer
JUP hsa05221    Acute myeloid leukemia
JUP hsa05226    Gastric cancer
JUP hsa05412    Arrhythmogenic right ventricular cardiomyopathy (ARVC)
ADD REPLYlink 20 months ago
cpad0112
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thanks for your response ;)

it is really helpful

ADD REPLYlink 20 months ago
EFN
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Hi again,

new question has arisen for me when I import a gene name that kegg cannot recognize it... the error is : if 'PATHWAY' in dic.keys(): AttributeError: 'int' object has no attribute 'keys'

I wrote an if statement, but the same error has occurred. where I'm doing wrong?

ADD REPLYlink 20 months ago
EFN
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well, it is a generic error by bioservices. If it can't find a match, it throws a general error. This is not an error in your input/code.

ADD REPLYlink 20 months ago
cpad0112
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GeneSCF will be handy for this task (NOT python).

ADD COMMENTlink 19 months ago EagleEye 6.4k
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