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Question: Help for pathway image: draw a KEGG pathway
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gravatar for wenfayuan
4 months ago by
wenfayuan • 10
wenfayuan • 10 wrote:

Hi, I have a list of genes generated from ucsc genome browser and output directly to Galaxy. I tried to use pathway image: draw a KEGG pathway, I have specified the columns with KEGG gene ID and KEGG pathway. But under the "pathway" states" Parameter pathway requires a value, but has no legal values defined". So what kind of value should I choose to put here? Thanks a lot!
pathway input kegg galaxy gene • 280 views
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modified 4 months ago by Jennifer Hillman Jackson ♦ 25k • written 4 months ago by wenfayuan • 10
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gravatar for Jennifer Hillman Jackson
4 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Include the pathway to graph on the tool form under the option Pathway (in addition to selecting the correct Column with KEGG gene ID/pathways). This will extract all entries that include that pathway in the output.

From the tool form help: Pathway Image : Draw a KEGG pathway, highlighting specified gene modules (Galaxy Version 1.1.0)

Note that cfa05214 is specified distinctly plus included in the 4th example input pathway column.

Example

input:

476153  probably damaging       cfa00230=Purine metabolism.cfa00500=Starch and sucrose metabolism.cfa00740=Riboflavin metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways
483960  probably damaging       N
610160  possibly damaging       N
403657  benign  cfa04010=MAPK signaling pathway.cfa04012=ErbB signaling pathway.cfa04060=Cytokine-cytokine receptor interaction.cfa04144=Endocytosis.cfa04510=Focal adhesion.cfa04540=Gap junction.cfa04810=Regulation of actin cytoskeleton.cfa05160=Hepatitis C.cfa05200=Pathways in cancer.cfa05212=Pancreatic cancer.cfa05213=Endometrial cancer.cfa05214=Glioma.cfa05215=Prostate cancer.cfa05218=Melanoma.cfa05219=Bladder cancer.cfa05223=Non-small cell lung cancer
etc.

output showing pathway cfa05214

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson ♦ 25k
1

Thank you very much!

ADD REPLY • link written 3 months ago by wenfayuan • 10
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