How do I do pathview analysis to get Kegg pathways with DEG lists

0

Entering edit mode

3.7 years ago

ashwing.kofficial ▴ 10

Hello everyone, I have the DEG list of gene name of upregulated and downregulated genes, I want to upload this data into pathview to get the kegg pathways but I am not able to because there is some other data type which is acceptable for pathview. Does anyone know how I can do it or suggest any alternatives for pathview to get kegg pathways for the dataset. I am not proficient at coding and did my rna-seq through galaxy so I am looking for something simple. But even if it is complex, I am okay with it cause I have been with this problem for weeks. Hoping for your response.

rna-sequencing Pathview • 1.5k views

ADD COMMENT • link 3.7 years ago by ashwing.kofficial ▴ 10

0

Entering edit mode

There are a couple simple to use internet programs that can do this + geneontology.

DAVID: https://david.ncifcrf.gov/tools.jsp

PANTHER: http://pantherdb.org/

g:Profiler: https://biit.cs.ut.ee/gprofiler/gost

ADD REPLY • link 3.7 years ago by noahhelton98 ▴ 80

0

Entering edit mode

Thanks a lot for your comment. But this is what I am looking for ,where my genes are highlighted so that I can understand it faster and better. I have seen for other options but only pathview offers such an option. If you have any platform which can give me this result, please let me know enter image description here

ADD REPLY • link 3.7 years ago by ashwing.kofficial ▴ 10

Login before adding your answer.