User: Ed

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Ed230
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Posts by Ed

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Comment: C: information retrieval from pubmed
... Thanks Julian and Steve. But I think I am more concerned with some results like after information retrieval, kind of a one step before text mining. So those genes after retrieval might just be "associated" with cancer. Is there some online tools to extract those info from like pubmed? Best, Nick ...
written 3.6 years ago by Ed230
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information retrieval from pubmed
... Hi there, I am wondering if there is a tool (in bioconductor or not, off-topic I am sorry) that can help me retrieve, for example, all gene symbols that appears in cancer biology in the journals of the last 5 years? Many thanks! Nick [[alternative HTML version deleted]] ...
cancer written 3.6 years ago by Ed230 • updated 3.6 years ago by Steve Lianoglou12k
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Comment: C: Change enzyme code (EC) into gene symbol
... Hi I think I figured that out by setting kegg.native = T, same.layer = F; Oops, I think I just did not understand your email very well :( Thanks a lot! But one more question, how do you treat multiple isoforms of an enzyme for one EC code in the package? Weiwei On Sat, Aug 31, 2013 at 4:12 PM ...
written 4.3 years ago by Ed230
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Comment: C: Change enzyme code (EC) into gene symbol
... Can I use gene symbol but keep a native KEGG view? I mean, I just want to replace the EC code with gene symbol without changing the layout or view of KEGG pathway? Thanks, weiwei On Thu, Aug 29, 2013 at 11:27 AM, Luo Weijun wrote: > Hi Weiwei, > Yes, you can get gene symbol instead of E ...
written 4.3 years ago by Ed230
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Comment: C: Change enzyme code (EC) into gene symbol
... Sure. Thanks. Actually I followed a couple of emails of a discussion of package called pathview but I changed the subject so it seemed an independent question to the forum and forgot to mention the background. On Tue, Aug 27, 2013 at 10:48 PM, Marc Carlson wrote: > Hi WeiWei, > > I do ...
written 4.3 years ago by Ed230
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Change enzyme code (EC) into gene symbol
... Hi there, I am wondering if you can change the ECs for each enzyme on the kegg graph like pyrimidine metabolism into gene symbol, for example? thanks, Weiwei [[alternative HTML version deleted]] ...
written 4.3 years ago by Ed230 • updated 4.3 years ago by Luo Weijun1.4k
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Comment: C: Pathview for global and overview maps Re: using pathview about hsa01100
... Yes. I agree. Actually I just want to touch the nodes (compounds) but I need to find how to know the ids (used on that map) for the substrate/product of an enzyme. Any idea? Thanks, Weiwei On Fri, Aug 16, 2013 at 5:26 PM, Luo Weijun wrote: > I don’t think pathview will do that. You will ...
written 4.3 years ago by Ed230
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Answer: A: Pathview for global and overview maps Re: using pathview about hsa01100
... Hi Weijun, It is one step away from what I want. However, I am wondering if, for example, I have an enzyme and would like to highlight its substrate and product, is it possible to do so? For example NME3 in pyrimidine metabolic pathway, I want to highlight its substrate and product in such global m ...
written 4.3 years ago by Ed230
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about running gsva on mac
... Hi there, I used the examples in ?gsva and got the following errors on my mac. However, I run it also on the linux and it worked. Please suggest. Thanks, Weiwei > library(limma) > > p <- 10 ## number of genes > n <- 30 ## number of samples > nGrp1 <- 15 ## number of samp ...
process gsva written 4.4 years ago by Ed230 • updated 4.4 years ago by Devon Ryan200
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using pathview about hsa01100
... Hi Weijun, In terms of the topmost metabolic pathway "hsa01100", I would like to highlight some enzymes on this pathway, however, it seems the "circles" on the plot are metabolites instead of enzymes. The enzymes are the "edges" on the plot. Do you know how to deal with this question? Alternative ...
written 4.4 years ago by Ed230 • updated 4.4 years ago by Luo Weijun1.4k

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