FAQ
1.) Does PhosNetVis require the users to login?
No PhosNetVis does not require you to login.
2.) What are alternative tools to fKSEA for conducting kinase-substrate enrichment analysis?
Some other tools commonly used in the literature are KSEA,KEA3,RoKAI App,KSEA professional and PhosFate.
3.) What is phosphorylation and why is it important?
Phosphorylation is a process where a phosphate group is added to a protein. This tiny modification can have major effects:
· Turning Proteins On and Off: Phosphorylation can activate or deactivate proteins, controlling their function in cells.
· Cell Communication: It helps cells talk to each other by regulating signals sent between them.
· Cell Growth and Division: Phosphorylation is crucial for regulating cell growth, division, and other important processes.
· Gene Expression: It can influence which genes are turned on or off, impacting how cells behave and respond to their environment.
· Metabolism: Phosphorylation plays a role in how cells use energy and process nutrients.
In essence, phosphorylation is a molecular switch that helps cells respond to changes in their surroundings and carry out their functions properly.
4.) What is a Kinase Substrate Interaction (KSI) network?
A KSI network shows how kinases (special proteins) interact with other proteins called substrates. Kinases help regulate many activities inside cells by adding a phosphate group to substrates. These interactions are like connections in a network, where each kinase is linked to the proteins it affects. By studying this network, scientists can understand how cells work and find new ways to treat diseases.
5.) Does PhosNetVis store data on a server?
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.
6.) I have my data in gene ID format instead of Protein ID format. Can I still use PhosNetvis?
Yes, absolutely! For fKSEA analyses, you need to first convert the gene IDs to Protein Accession IDs using an API such as UniProt. 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.