Find Kegg Pathway That Contain Certain Genes

Question

[NetunoPoncã]

Hi,

I have a file that contains multiple gene lists (triples of genes). For each triple I want to know if there is a KEGG pathway that contains all the three genes (from yeast). Actually I am dealing with genes and protein names, as far as i know. For example, I have:

Line1: ACC1 YKU80 DPB2 Line2: ACC1 YKU80 TPS1 Line3: SIT4 CCT6 CCR4

I want to know which pathways contain all the three IDS from Line1, Line2 and so on...

I know that from http://www.genome.jp/kegg/tool/map_pathway2.html I can get such pathways, but my file is big... I'm trying to use KEGG API with no success. I'm using function "serv.getpathwaysby_genes" but I always get a empty results...

Can someone help me pls?

Answer 1

[Giovanni M Dall'Olio]

Try Enrichnet. Paste the genes on the input box, press continue, and on the second page you will be able to choose KEGG as query database.

To do this programmatically, you can use their APIs (link to API documentation). You can build a link like http://bree.cs.nott.ac.uk/enrichnet/index.php?genes=MOGS_HUMANALG3_HUMAN&idtype=uniprot_swissprot&pathdb=kegg&graph=bossi (which you can retrieve with wget, for example), or even easier, you can use the python script in the documentation and adapt it to a loop.

Answer 2

[mgalactus]

Use the KEGG API, using many requests using just one gene: I think that when you provide multiple gene identifiers it returns the pathways that contain ALL the genes you provided.

Answer 3

[NetunoPoncã]

Actually I'm using the API but I think the problem is the gene/protein IDS... KEGG is not recognizing them when I use the API... On the other hand, if i use the website they are recognized...

Dont know what to do :(

[Obi Griffith]

Hi Pablo. Welcome to Biostar! In future, when responding to people's answers please respond as comments to their answer or by editing your original question rather than creating a new answer which is really a response to an answer.