User: lucatucciarone

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Posts by lucatucciarone

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Comment: C: Link pathways to Gene Onthologies from RNA-seq differential expressed genes
... Unfortunately not, it's from the IPA knowledgeabase. I wanna say I'm not married to IPA, I can definitely switch to another tool if it would allow me to do what I'd like to : ) ...
written 1 day ago by lucatucciarone50
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Comment: C: Link pathways to Gene Onthologies from RNA-seq differential expressed genes
... Hello Jared! Thanks for helping me again : ) I got my pathways from IPA. Unfortunately though, IPA doesn't give me a clear idea of what biological process a specific pathway is activating or inhibiting. What I'd like to do is: 1) Performing Pathway analysis using the differentially expressed ge ...
written 2 days ago by lucatucciarone50
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Link pathways to Gene Onthologies from RNA-seq differential expressed genes
... Hello everybody! I was thinking whether existed a way to link a pathway to a GO-term (Biological process). For example, let's say I have MTOR signalling activated, I know from the literature that is linked with cell growth. Is there a way to compute all those relationships? Thanks! ...
rna-seq written 2 days ago by lucatucciarone50
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Comment: C: Visualize overlap differentially expressed genes of multiple comparisons.
... This seems more doable. Would you mind uploading a sample picture to see how it turn out? ...
written 4 days ago by lucatucciarone50
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Comment: C: Visualize overlap differentially expressed genes of multiple comparisons.
... mmmh that's a good idea, I've already used them. There is nothing specific for up and down regulated genes though? ...
written 4 days ago by lucatucciarone50
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Visualize overlap differentially expressed genes of multiple comparisons.
... Hello everyone, I need to represent the overlap of differentially expressed genes across multiple comparisons. Essentially, I have the log2foldchange of my 4 samples (Control, Treatment 1, 2, 3). Obviously my comparisons are Control vs Treatment 1 Control vs Treatment 2 Control vs Treatment 3 C ...
rna-seq written 4 days ago by lucatucciarone50
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Gene ontology for biological processes from differentially expressed genes
... This is a post to better understand what is your favorite tool to perform gene ontology for biological processes from differentially expressed genes (RNA-seq Data). There are a lot of tools over the internet, for now I'm been using IPA (Luckily my institute has a subscription) but I find it someti ...
rna-seq written 12 days ago by lucatucciarone50
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Comment: C: Pathway based data integration and Visualization with gene ortholog
... What do you mean? I can Post my script if you need it ...
written 11 weeks ago by lucatucciarone50
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Comment: C: Pathway based data integration and Visualization with gene ortholog
... Oh my, Oh my. Thank you so much. As always it was very simple. Solved!!! ...
written 3 months ago by lucatucciarone50
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Pathway based data integration and Visualization with gene ortholog
... I would like to visualize my RNA-seq data (Mouse) on a KEGG pathway that seem to be present only for Humans (hsa04623). I'm trying using Pathview, it works beautifully with Human datasets but I don't see any way to make it work with my Murine one using a human pathway. There is indeed support fo ...
R rna-seq written 3 months ago by lucatucciarone50 • updated 12 weeks ago by Biostar ♦♦ 20

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