Question: How to do simple pathway analysis?
0
gravatar for Seq225
16 months ago by
Seq22590
Seq22590 wrote:

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 gene genome • 679 views
ADD COMMENTlink modified 16 months ago by AK1.9k • written 16 months ago by Seq22590

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

ADD REPLYlink written 16 months ago by hafiz.talhamalik240
1
gravatar for AK
16 months ago by
AK1.9k
AK1.9k wrote:

Hi Seq225, I did it in 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
#

  KEGG Orthology (KO)

! 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.

ADD COMMENTlink modified 16 months ago • written 16 months ago by AK1.9k
1

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

ADD REPLYlink modified 16 months ago • written 16 months ago by AK1.9k
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