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?
•
written
by
parvathi.sudha •
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
Thank you for your help. Is there any way to get the pathway list for the genes?
$ kg -s hsa -d | grep "CDK4\b" | head -3 04110 CDK4 Cell cycle 04115 CDK4 p53 signaling pathway 04151 CDK4 PI3K-Akt signaling pathway
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; doneThanks. 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.
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written
by
parvathi.sudha •
Hi, actually, you should post this as comments because these are not answers.
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written
by
Prakki Rama
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Erm, KEGG is supposed to be non-hierarchical. Are you sure there actually are any subpathways in kegg?
If you want the pathway to gene maps, this is trivial to do in kg (
pip install kg):See https://github.com/endrebak/kg for more
By sub pathway, I meant those (example: signaling) pathways which are mentioned in a cancer pathway.
To get pathway list for genes, submit the fasta file in KEGG Automatic Annotation Server (KAAS).