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Update FAQ.md
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oshorawal authored Nov 6, 2024
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FAQ
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<b>1.) Does PhosNetVis requires the users to login?</b>
<b>1.) Does PhosNetVis require the users to login?</b>
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No PhosNetVis does not requires you to login.
No PhosNetVis does not require you to login.
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<b>2.) What are some other tools which can be used for doing Kinase-substrate enrichment analysis?</b>
<b>2.) What are alternative tools to fKSEA for conducting kinase-substrate enrichment analysis?</b>
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If the users have GeneId and residue Ids then <a href="https://casecpb.shinyapps.io/ksea/" target="_blank">KSEA tool</a> can be used. Some other tools are <a href="https://maayanlab.cloud/kea3/" target="_blank">KEA3</a> and <a href="https://github.com/CutillasLab/KSEA_professional" target="_blank">KSEA professional</a>.
Some other tools commonly used in the literature are <a href="https://casecpb.shinyapps.io/ksea/" target="_blank">KSEA</a>,<a href="https://maayanlab.cloud/kea3/" target="_blank">KEA3</a> and <a href="https://github.com/CutillasLab/KSEA_professional" target="_blank">KSEA professional</a>.
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<b>3.) What is phosphorylation and why is it important?</b>
Expand All @@ -35,5 +35,12 @@ A KSI network shows how kinases (special proteins) interact with other proteins
<b>5.) Does PhosNetVis store data on a server?</b>
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PhosnetVis runs on the client browser window. All modules except fGSEA(fast gene-set enrichment algorithm) run on the local browser. For fGSEA, the data are sent to a HIPAA-compliant server at the Icahn School of Medicine, through a HTTPS protocol which is safe and secure. Once the fGSEA is run, no data is stored on the server.
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<b>6.) I have my data in gene ID format instead of Protein ID format. Can I still use PhosNetvis?</b>
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Yes, absolutely! For fKSEA analyses, you need to first convert the gene IDs to Protein Accession IDs using an API such as <a href="https://www.uniprot.org/id-mapping" target="_blank">UniProt</a>. Then, you can run fKSEA analysis. For Network Visualization, you can upload your data in gene ID format directly to the "Upload Data for Visualization" section.
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