Extract list of genes from a KEGG sub pathways

Question

[parvathi.sudha]

Hi,

I am trying to extract the pathway level information from different cancer pathways. I need to get the genes involved in all the sub pathways,

For example: Considering the NSCLC pathway (hsa05223 - non-small cell lung cancer), there are different types of pathways inside them; like, Calcium -signaling pathway, MAPK pathway etc. I want to get the list of those genes for studying the pathway cross talk.

Can anyone know, how to get those list?

[Endre Bakken Stovner]

Erm, KEGG is supposed to be non-hierarchical. Are you sure there actually are any subpathways in kegg?

[Endre Bakken Stovner]

If you want the pathway to gene maps, this is trivial to do in kg (pip install kg):

$ kg -s hsa | grep 05223 | head -3
05223    STK-2
05223    RAC-gamma
05223    RAC-PK-gamma

See https://github.com/endrebak/kg for more

[parvathi.sudha]

By sub pathway, I meant those (example: signaling) pathways which are mentioned in a cancer pathway.

[Prakki Rama]

To get pathway list for genes, submit the fasta file in KEGG Automatic Annotation Server (KAAS).

Answer 1

[5heikki]

curl http://rest.kegg.jp/link/genes/hsa05223
path:hsa05223    hsa:10000
path:hsa05223    hsa:1019
path:hsa05223    hsa:1021
path:hsa05223    hsa:1029
path:hsa05223    hsa:11186
path:hsa05223    hsa:1869
path:hsa05223    hsa:1870
path:hsa05223    hsa:1871
path:hsa05223    hsa:1950
path:hsa05223    hsa:1956
path:hsa05223    hsa:2064
path:hsa05223    hsa:207
path:hsa05223    hsa:208
path:hsa05223    hsa:2272
path:hsa05223    hsa:2309
path:hsa05223    hsa:23533
path:hsa05223    hsa:238
path:hsa05223    hsa:27436
path:hsa05223    hsa:2885
path:hsa05223    hsa:3265
path:hsa05223    hsa:369
path:hsa05223    hsa:3845
path:hsa05223    hsa:4893
path:hsa05223    hsa:5170
path:hsa05223    hsa:5290
path:hsa05223    hsa:5291
path:hsa05223    hsa:5293
path:hsa05223    hsa:5294
path:hsa05223    hsa:5295
path:hsa05223    hsa:5296
path:hsa05223    hsa:5335
path:hsa05223    hsa:5336
path:hsa05223    hsa:5578
path:hsa05223    hsa:5579
path:hsa05223    hsa:5582
path:hsa05223    hsa:5594
path:hsa05223    hsa:5595
path:hsa05223    hsa:5604
path:hsa05223    hsa:5605
path:hsa05223    hsa:572
path:hsa05223    hsa:5894
path:hsa05223    hsa:5915
path:hsa05223    hsa:5925
path:hsa05223    hsa:595
path:hsa05223    hsa:6256
path:hsa05223    hsa:6257
path:hsa05223    hsa:6258
path:hsa05223    hsa:6654
path:hsa05223    hsa:6655
path:hsa05223    hsa:673
path:hsa05223    hsa:6789
path:hsa05223    hsa:7039
path:hsa05223    hsa:7157
path:hsa05223    hsa:83593
path:hsa05223    hsa:842
path:hsa05223    hsa:8503

http://www.kegg.jp/kegg/docs/keggapi.html

[parvathi.sudha]

Thank you for your help. Is there any way to get the pathway list for the genes?

[Endre Bakken Stovner]

$ kg -s hsa -d | grep "CDK4\b" | head -3
04110    CDK4    Cell cycle
04115    CDK4    p53 signaling pathway
04151    CDK4    PI3K-Akt signaling pathway

[5heikki]

curl http://rest.kegg.jp/link/pathway/hsa:10000
hsa:10000 path:hsa04010
hsa:10000 path:hsa04012
hsa:10000 path:hsa04014
hsa:10000 path:hsa04015
hsa:10000 path:hsa04022
hsa:10000 path:hsa04024
hsa:10000 path:hsa04062
..

curl http://rest.kegg.jp/link/pathway/hsa:1019
hsa:1019 path:hsa04110
hsa:1019 path:hsa04115
hsa:1019 path:hsa04151
hsa:1019 path:hsa04530
hsa:1019 path:hsa04660
hsa:1019 path:hsa05161
..

etc.

So, for example:

for next in $(curl http://rest.kegg.jp/link/genes/hsa05223 | cut -f2 -d $'\t' | sort -u); do curl http://rest.kegg.jp/link/pathway/$next > $next.list; done

[parvathi.sudha]

Thanks. Got another way to solve using KEGGREST.

path = keggLink("hsa", "pathway")

But, having a problem in splitting it. "path" is stored as character.

I am newbie in programming. Appreciate if someone replies with the code.

[Prakki Rama]

Hi, actually, you should post this as comments because these are not answers.

Answer 2

[EagleEye]

This might be helpful 1) How to interpret the result of GO analysis using Ontologizer / mapping GO IDs to GO TERMS ? 2) https://github.com/santhilalsubhash/geneSCF/tree/master/annotation