Question: Extract list of genes from a KEGG sub pathways
0
gravatar for parvathi.sudha
4.0 years ago by
United States
parvathi.sudha0 wrote:

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 • 2.3k views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by parvathi.sudha0

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

ADD REPLYlink written 4.0 years ago by Endre Bakken Stovner880

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 REPLYlink written 4.0 years ago by Endre Bakken Stovner880

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

ADD REPLYlink written 4.0 years ago by parvathi.sudha0

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

ADD REPLYlink written 4.0 years ago by Prakki Rama2.3k
1
gravatar for 5heikki
4.0 years ago by
5heikki8.5k
Finland
5heikki8.5k wrote:
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 COMMENTlink written 4.0 years ago by 5heikki8.5k
0
gravatar for parvathi.sudha
4.0 years ago by
United States
parvathi.sudha0 wrote:

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

ADD COMMENTlink written 4.0 years ago by parvathi.sudha0
$ 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 REPLYlink written 4.0 years ago by Endre Bakken Stovner880
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 REPLYlink modified 4.0 years ago • written 4.0 years ago by 5heikki8.5k
0
gravatar for EagleEye
4.0 years ago by
EagleEye6.5k
Sweden
EagleEye6.5k wrote:
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
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by EagleEye6.5k
0
gravatar for parvathi.sudha
4.0 years ago by
United States
parvathi.sudha0 wrote:

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 COMMENTlink written 4.0 years ago by parvathi.sudha0

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

ADD REPLYlink written 4.0 years ago by Prakki Rama2.3k
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