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How to do simple pathway analysis?

I have a set of 100 genes (the AA sequences) from a non-model plant species. Now I want to simply identify which pathways they belong to. I want to generate a typical KEGG style image/map highlighting my genes in the entire pathway.

I want to identify my genes that cluster in the same pathway.

How can I do that? I don't know much about KEGG or any other tools.

Thanks a lot!!

rna-seq genome gene
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updated by he1k • he1k • written by Seq225 Seq225

you can use simply use web based kegg database and also you can use david tool as well

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written by hafiz.talhamalik hafiz.talhamalik

1 answer

Hi Seq225, I did it this way:

  1. Annotate the AA sequences using the web service BlastKOALA (see Step-by-step Instructions);
  2. Download the hierarchical data containing KOs and pathways from KEGG and save as "KO.keg";
  3. Parse "KO.keg" into tidy format ("KO.tsv");
  4. Join your KO assignment results (from step1) with "KO.tsv", then you'll see which genes are clustered in the same pathway.
$ wget -O KO.keg "http://www.genome.jp/kegg-bin/download_htext?htext=ko00001.keg&format=htext&filedir="
$ head KO.keg
+D  KO
#<h2><a href="/kegg/kegg2.html"><img src="/Fig/bget/kegg3.gif" align="middle" border=0></a>   KEGG Orthology (KO)</h2>
!
A09100 Metabolism
B
B  09101 Carbohydrate metabolism
C    00010 Glycolysis / Gluconeogenesis [PATH:ko00010]
D      K00844  HK; hexokinase [EC:2.7.1.1]
D      K12407  GCK; glucokinase [EC:2.7.1.2]
D      K00845  glk; glucokinase [EC:2.7.1.2]

$ head KO.tsv
09100   Metabolism  09101   Carbohydrate metabolism 00010   Glycolysis / Gluconeogenesis    K00844  HK  hexokinase  EC:2.7.1.1
09100   Metabolism  09101   Carbohydrate metabolism 00010   Glycolysis / Gluconeogenesis    K12407  GCK glucokinase EC:2.7.1.2
09100   Metabolism  09101   Carbohydrate metabolism 00010   Glycolysis / Gluconeogenesis    K00845  glk glucokinase EC:2.7.1.2
09100   Metabolism  09101   Carbohydrate metabolism 00010   Glycolysis / Gluconeogenesis    K01810  GPI, pgi    glucose-6-phosphate isomerase   EC:5.3.1.9
09100   Metabolism  09101   Carbohydrate metabolism 00010   Glycolysis / Gluconeogenesis    K06859  pgi1    glucose-6-phosphate isomerase, archaeal EC:5.3.1.9
09100   Metabolism  09101   Carbohydrate metabolism 00010   Glycolysis / Gluconeogenesis    K13810  tal-pgi transaldolase / glucose-6-phosphate isomerase   EC:2.2.1.2 5.3.1.9
09100   Metabolism  09101   Carbohydrate metabolism 00010   Glycolysis / Gluconeogenesis    K15916  pgi-pmi glucose/mannose-6-phosphate isomerase   EC:5.3.1.9 5.3.1.8
09100   Metabolism  09101   Carbohydrate metabolism 00010   Glycolysis / Gluconeogenesis    K00850  pfkA, PFK   6-phosphofructokinase 1 EC:2.7.1.11
09100   Metabolism  09101   Carbohydrate metabolism 00010   Glycolysis / Gluconeogenesis    K16370  pfkB    6-phosphofructokinase 2 EC:2.7.1.11

Hope it helps.

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written by AK AK

I revisited it and found a simpler way:

  • Submit your AA sequences to KofamKOALA;
  • When the job is done you'll receive an URL for the report. In that web page report, click "KEGG Mapper" followed by "Reconstruct Pathway". You'll see your AA sequences clustered under each pathway:

Pathway Reconstruction

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written by AK AK

Hi AK,

I downloaded the KO.keg file. I was wondering what tool(s) you used to generate the "KO.tsv" file as you showed here. Thanks.

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written by he1k • he1k

Hi he1k,

Please use the following script which downloads and parses the keg data on the fly: keg_hierarchy_parser.py

Hope this helps!

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written by AK AK

Hi AK,

Thanks very much for sharing the script. It is very helpful. I really appreciate it.

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written by he1k • he1k

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