Question

how to build gene.pathway data.frame for non-model organism

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mictadlo ▴ 10

@mictadlo-10885

Last seen 4.3 years ago

Hello,

I have been pointed out A: How to use topGO and KEGG with de-novo species that is possible to use how to use "non-standard" species for KEGG / GO analysis in limma? to do any analysis, including KEGG or GO analyses of a new species.

How is it possible to create an annotation database using annotationHub() or by supplying the gene.pathway data.frame directly for my non-model species?

Thank you in advance.

limma kegg topgo dataframe edger • 1.2k views

ADD COMMENT • link 6.6 years ago mictadlo ▴ 10

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One obviously needs a mapping between your organism's genes and the pathway that those genes belong to. Where that mapping comes from depends of course on the organism, and probably you are in the best position to identify this source. Minimally, adding, as a COMMENT, the organism that you are working on is essential for others to help you make progress here.

ADD REPLY • link 6.6 years ago Martin Morgan 25k

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It is a non model plant genome and I ran edgeR and I have a the following genome annotation file:

lcl|ScwjSwM_6572    maker    gene    14106    17663    .    -    .    ID=sp0000006;Name=sp0000006
lcl|ScwjSwM_6572    maker    mRNA    14106    17663    .    -    .    ID=sp0000006-mRNA-1;Parent=sp0000006;Name=sp0000006-mRNA-1;_AED=0.16;_eAED=0.16;_QI=299|0.71|0.62|1|0.57|0.37|8|395|282
lcl|ScwjSwM_6572    maker    mRNA    14106    17663    .    -    .    ID=sp0000006-mRNA-2;Parent=sp0000006;Name=sp0000006-mRNA-2;_AED=0.16;_eAED=0.16;_QI=299|0.66|0.57|1|0.66|0.57|7|415|282
lcl|ScwjSwM_6572    maker    mRNA    14106    17663    .    -    .    ID=sp0000006-mRNA-3;Parent=sp0000006;Name=sp0000006-mRNA-3;_AED=0.19;_eAED=0.19;_QI=299|1|0.85|1|0.83|0.71|7|395|235
lcl|ScwjSwM_6572    maker    exon    14752    14871    .    -    .    ID=sp0000006-mRNA-3:exon:276;Parent=sp0000006-mRNA-3
lcl|ScwjSwM_6572    maker    exon    15581    15745    .    -    .    ID=sp0000006-mRNA-3:exon:275;Parent=sp0000006-mRNA-3
...
lcl|ScwjSwM_6572    maker    exon    17152    17188    .    -    .    ID=sp0000006-mRNA-1:exon:267;Parent=sp0000006-mRNA-1,sp0000006-mRNA-2,sp0000006-mRNA-3
lcl|ScwjSwM_6572    maker    exon    17331    17663    .    -    .    ID=sp0000006-mRNA-1:exon:266;Parent=sp0000006-mRNA-1,sp0000006-mRNA-2,sp0000006-mRNA-3
lcl|ScwjSwM_6572    maker    five_prime_UTR    17365    17663    .    -    .    ID=sp0000006-mRNA-1:five_prime_utr;Parent=sp0000006-mRNA-1
lcl|ScwjSwM_6572    maker    CDS    17331    17364    .    -    0    ID=sp0000006-mRNA-1:cds;Parent=sp0000006-mRNA-1
...
lcl|ScwjSwM_6572    maker    CDS    14752    14874    .    -    0    ID=sp0000006-mRNA-1:cds;Parent=sp0000006-mRNA-1
lcl|ScwjSwM_6572    maker    CDS    14521    14658    .    -    0    ID=sp0000006-mRNA-1:cds;Parent=sp0000006-mRNA-1
lcl|ScwjSwM_6572    maker    three_prime_UTR    14516    14520    .    -    .    ID=sp0000006-mRNA-1:three_prime_utr;Parent=sp0000006-mRNA-1
lcl|ScwjSwM_6572    maker    three_prime_UTR    14106    14495    .    -    .    ID=sp0000006-mRNA-1:three_prime_utr;Parent=sp0000006-mRNA-1
lcl|ScwjSwM_6572    maker    five_prime_UTR    17365    17663    .    -    .    ID=sp0000006-mRNA-2:five_prime_utr;Parent=sp0000006-mRNA-2
lcl|ScwjSwM_6572    maker    CDS    17331    17364    .    -    0    ID=sp0000006-mRNA-2:cds;Parent=sp0000006-mRNA-2
lcl|ScwjSwM_6572    maker    CDS    17152    17188    .    -    2    ID=sp0000006-mRNA-2:cds;Parent=sp0000006-mRNA-2
...
lcl|ScwjSwM_6572    maker    CDS    14521    14658    .    -    0    ID=sp0000006-mRNA-2:cds;Parent=sp0000006-mRNA-2
lcl|ScwjSwM_6572    maker    three_prime_UTR    14106    14520    .    -    .    ID=sp0000006-mRNA-2:three_prime_utr;Parent=sp0000006-mRNA-2
lcl|ScwjSwM_6572    maker    five_prime_UTR    17365    17663    .    -    .    ID=sp0000006-mRNA-3:five_prime_utr;Parent=sp0000006-mRNA-3
lcl|ScwjSwM_6572    maker    CDS    17331    17364    .    -    0    ID=sp0000006-mRNA-3:cds;Parent=sp0000006-mRNA-3
...
lcl|ScwjSwM_6572    maker    CDS    14521    14658    .    -    0    ID=sp0000006-mRNA-3:cds;Parent=sp0000006-mRNA-3
lcl|ScwjSwM_6572    maker    three_prime_UTR    14516    14520    .    -    .    ID=sp0000006-mRNA-3:three_prime_utr;Parent=sp0000006-mRNA-3
lcl|ScwjSwM_6572    maker    three_prime_UTR    14106    14495    .    -    .    ID=sp0000006-mRNA-3:three_prime_utr;Parent=sp0000006-mRNA-3

and the following interproscan file:

sp0000006-mRNA-1    edf5c2bb6341fe44b3da447099a5b2df    282    Pfam    PF03083    Sugar efflux transporter for intercellular exchange    198    261    1.4E-15    T    02-05-2017    IPR004316    SWEET sugar transporter    GO:0016021
sp0000006-mRNA-1    edf5c2bb6341fe44b3da447099a5b2df    282    Pfam    PF03083    Sugar efflux transporter for intercellular exchange    7    91    1.1E-25    T    02-05-2017    IPR004316    SWEET sugar transporter    GO:0016021
sp0000006-mRNA-2    edf5c2bb6341fe44b3da447099a5b2df    282    Pfam    PF03083    Sugar efflux transporter for intercellular exchange    198    261    1.4E-15    T    02-05-2017    IPR004316    SWEET sugar transporter    GO:0016021
sp0000006-mRNA-2    edf5c2bb6341fe44b3da447099a5b2df    282    Pfam    PF03083    Sugar efflux transporter for intercellular exchange    7    91    1.1E-25    T    02-05-2017    IPR004316    SWEET sugar transporter    GO:0016021
sp0000006-mRNA-3    51ff56e496d48682f7af1b2478190834    235    Pfam    PF03083    Sugar efflux transporter for intercellular exchange    130    214    9.6E-24    T    02-05-2017    IPR004316    SWEET sugar transporter    GO:0016021
sp0000006-mRNA-3    51ff56e496d48682f7af1b2478190834    235    Pfam    PF03083    Sugar efflux transporter for intercellular exchange    7    91    7.5E-26    T    02-05-2017    IPR004316    SWEET sugar transporter    GO:0016021

ADD REPLY • link 6.6 years ago mictadlo ▴ 10