Question: KEGG Pathway elements' text color code
0
gravatar for komal.rathi
2.6 years ago by
komal.rathi2.9k
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi2.9k wrote:

When looking at the KEGG Pathways, why is the text of some proteins red? Why are others colored as black? For e.g. if you click here, some proteins like SGCD, Desmin & DMD are highlighted in red text while others like ITGA, ITGB, ACTG1 etc have a black text. I clicked on a couple of proteins to find out the difference, but it all looks pretty much the same to me. 

kegg pathway • 1.4k views
ADD COMMENTlink written 2.6 years ago by komal.rathi2.9k

Usually when a user provide a list of genes to find out a KEGG pathway , the database list out the entire pathway and the genes which are present in the user list are highlighted in red. So I would assume that the red ones in the link are the genes which is user supplied.

ADD REPLYlink written 2.6 years ago by vchris_ngs4.0k

I actually did not supply any genes to KEGG. You can try searching for other pathways on KEGG without supplying a gene list. I am pretty sure you will see some genes highlighted in red.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by komal.rathi2.9k
1
gravatar for vchris_ngs
2.6 years ago by
vchris_ngs4.0k
Milan, Italy
vchris_ngs4.0k wrote:

I tried to dig a bit more into the KEGG pathways and what I observed is for pathways like cancer its showing the ones in red which are oncogenes and are associated with humans, however if you look at other pathways which are under Metabolism, Nervous system or Organismal ( all others apart from Human diseases) you will not find the red color on the proteins. However in this link if you take a look you can see they are mentioned as oncogenes or tumor suppressor  genes (TSG) and I believe that the proteins which are in RED are in Human system that have been validated. I have tried to check the same in the other species for the same pathway and it shows red stating oncogenes and TSG . I believe the proteins which have already been experimentally validated in a pathway for human samples and reach some significance are highlighted in red. Similarly goes for the Desmin and DMD, probably they are the most important protein driving the pathway which have already been experimentally validated driving the majority of the signalling. This is what I understood after carefully looking at the different pathways in KEGG.

ADD COMMENTlink written 2.6 years ago by vchris_ngs4.0k
1

Wow, thanks for that. I think you should move this comment to an answer. I'd be happy to accept it. 

ADD REPLYlink written 2.6 years ago by komal.rathi2.9k

I already did that

ADD REPLYlink written 2.6 years ago by vchris_ngs4.0k

I think it would be more reasonable that those RED ones are mutant genes in their disease pathways.

ADD REPLYlink written 2.1 years ago by Ligaopeng20
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