Extract list of genes from a KEGG sub pathways
2
0
Entering edit mode
9.2 years ago

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?

KEGG-pathway • 4.4k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
9.2 years ago
5heikki 11k
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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
$ kg -s hsa -d | grep "CDK4\b" | head -3
04110    CDK4    Cell cycle
04115    CDK4    p53 signaling pathway
04151    CDK4    PI3K-Akt signaling pathway
ADD REPLY
0
Entering edit mode
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
ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1974 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6