Body: <p>I'm sorry for having such a juvenile question, but I'm still new in bioinformatics, and I was wondering whether there is any tool able to perform the task I'm dealing with now.
  Here is a short description (please let me know if more information should be provided from my side):</p>
  <p>I started with 3 genes of <em>Arabidopsis thaliana</em> (let me call them geneA, geneB, geneC). All of them are well annotated and they're known as transcription factors, but each is coming from different signaling pathway.</p>
  <p>My aim is to do this:</p>
  <ol>
  <li>To find all the signaling pathways related to each of these 3 genes (this is to identify which genes are the most upstream ones in each pathway*).</li>
  <li>Afterwards, let's say from all the found signaling pathways of the geneA, I only want to pick those that are sharing genes with the signaling pathways of the geneB and with the signaling pathways of the geneC.</li>
  </ol>
  <p>At the end, I would like to get a graphical visualization** of whether and how these signaling pathways are interconnected and what are the particular genes that are shared by those pathways.</p>
  <p>*) I cannot use the very popular tool called &quot;String&quot; from string-db.org because it <strong>doesn't show the sequence/order of the signaling</strong>.</p>
  <p>**) I know that KEGG is a database full of graphs of different metabolic patways, but in case of interconnections between <strong>signaling pathways in plants</strong>, it is either very poor tool, or I'm not that much able to find such a option there to do the job for me (even my colleagues didn't manage finding it).</p>
  <p>All of this would be probably more of a literature-mining type of work, but I'm quite sure that, at the end, my task will be to process not only 3 genes, but maybe even more than 10-20 genes. Thus, I would appreciate any more convenient way rather than just digging the info about each gene from the literature and drawing my graphs manually by hand. Automation in this case matters!</p>
  <p>Thanks for any help!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-08T06:43:58.800Z
Comments.Text: Is there any tool that will find signaling pathways that include one or more of my query genes and then graphically visualizes the possible interconnections between those pathways?
Comments.UserDisplayName: Tom
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-08T22:16:23.080Z
Comments.Text: i suggest reading more about regulatory network inference tools and related datasets https://www.frontiersin.org/articles/10.3389/fgene.2020.00457/full
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-09T09:28:03.203Z
Comments.Text: @MaximilianPress As far as I understand, such a tool I was looking for does not exist yet. I hope that soon I could find something like a interactive database of signaling pathways interactions. Anyways, thank you for help!
Comments.UserDisplayName: Tom
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-13T12:49:17.563Z
Comments.Text: I checked reactome, and that one does not seem to have plants at all. But then google "arabidopsis pathways" returned this https://www.arabidopsis.org/biocyc/? Could it work?
Comments.UserDisplayName: Kamil S Jaron
Tags: <interactions><graphs>
Title: Plant signaling pathway interconnections
ThreadText: # Plant signaling pathway interconnections
  
  (Asked by: username_0 on 2022-01-07)
  
  I'm sorry for having such a juvenile question, but I'm still new in bioinformatics, and I was wondering whether there is any tool able to perform the task I'm dealing with now.
  Here is a short description (please let me know if more information should be provided from my side):
  
  I started with 3 genes of *Arabidopsis thaliana* (let me call them geneA, geneB, geneC). All of them are well annotated and they're known as transcription factors, but each is coming from different signaling pathway.
  
  My aim is to do this:
  
  1. To find all the signaling pathways related to each of these 3 genes (this is to identify which genes are the most upstream ones in each pathway\*).
  2. Afterwards, let's say from all the found signaling pathways of the geneA, I only want to pick those that are sharing genes with the signaling pathways of the geneB and with the signaling pathways of the geneC.
  
  At the end, I would like to get a graphical visualization\*\* of whether and how these signaling pathways are interconnected and what are the particular genes that are shared by those pathways.
  
  \*) I cannot use the very popular tool called "String" from string-db.org because it **doesn't show the sequence/order of the signaling**.
  
  \*\*) I know that KEGG is a database full of graphs of different metabolic patways, but in case of interconnections between **signaling pathways in plants**, it is either very poor tool, or I'm not that much able to find such a option there to do the job for me (even my colleagues didn't manage finding it).
  
  All of this would be probably more of a literature-mining type of work, but I'm quite sure that, at the end, my task will be to process not only 3 genes, but maybe even more than 10-20 genes. Thus, I would appreciate any more convenient way rather than just digging the info about each gene from the literature and drawing my graphs manually by hand. Automation in this case matters!
  
  Thanks for any help!
  
  **Tags:** interactions, graphs
  
  > **Comments:**
  > **username_0**: Is there any tool that will find signaling pathways that include one or more of my query genes and then graphically visualizes the possible interconnections between those pathways?  
  > **username_1**: i suggest reading more about regulatory network inference tools and related datasets https://www.frontiersin.org/articles/10.3389/fgene.2020.00457/full  
  > **username_0**: @username_1 As far as I understand, such a tool I was looking for does not exist yet. I hope that soon I could find something like a interactive database of signaling pathways interactions. Anyways, thank you for help!  
  > **username_2**: I checked reactome, and that one does not seem to have plants at all. But then google "arabidopsis pathways" returned this https://www.arabidopsis.org/biocyc/? Could it work?  
  
  ---
  
  ## 0 answers
  
  