Ma'am, Could you please make a video on data mining for developing the network, how the bioactive screening are done, target ids and then merging it with disease databases and KEGG databases.
Hi Iam using cytoscape by cytohubba to make the networks of modules got from WGCNA analysis. When I try to make the network with the module having genes higher than 1000. It start asking “calculate scores of all nodes by 11 method” i try to cancel many times, but cancellation takes lots of time. What should I do ?
I tried to analyse my PPI network with bingo. But when i opened it in cytoscape, I could not extend it. The start button is below my laptop task bar. I tried to uphold that but couldnot. How can I solve that problem.
Thank you for your lecture. but i have a question you did not give any values I mean numeric that correlates the strength of connection of these nodes with each other then how can we predict that top ten nodes are these. i think this is not fair to do network without giving only nodes in formation and skipping the strength of these connections. please comment . thank you again
@@zohaibatif4008 To find hub nodes, you generally do not need numerical correlation directly. The centrality measures (degree, betweenness, closeness, etc.) depend on the structure of the network (connections between nodes), not the numerical correlations between node attributes. Numerical correlation may be useful for building or weighting the network (e.g., in gene co-expression networks), but the hub nodes are identified through network centrality, which focuses on the topological importance of nodes in the network. The CytoHubba tool in Cytoscape is used to rank nodes in a network based on their centrality or importance according to different algorithms (e.g., degree, betweenness, closeness, etc.). When CytoHubba generates a node ranking, the output is often saved as a CSV file.
Ma'am, Could you please make a video on data mining for developing the network, how the bioactive screening are done, target ids and then merging it with disease databases and KEGG databases.
Sure, stay updated will get notification for the same🙂
Hi Iam using cytoscape by cytohubba to make the networks of modules got from WGCNA analysis. When I try to make the network with the module having genes higher than 1000. It start asking “calculate scores of all nodes by 11 method” i try to cancel many times, but cancellation takes lots of time. What should I do ?
what type of network are you constructing PPIs?
@ to get the top 10 hub genes MCC method
I tried to analyse my PPI network with bingo. But when i opened it in cytoscape, I could not extend it. The start button is below my laptop task bar. I tried to uphold that but couldnot. How can I solve that problem.
Kindly use the String database string-db.org/ to analyze the PPI network.
mam please make a video on clustering 🙏
Sure
Thank you for your lecture. but i have a question you did not give any values I mean numeric that correlates the strength of connection of these nodes with each other then how can we predict that top ten nodes are these. i think this is not fair to do network without giving only nodes in formation and skipping the strength of these connections. please comment . thank you again
@@zohaibatif4008 To find hub nodes, you generally do not need numerical correlation directly. The centrality measures (degree, betweenness, closeness, etc.) depend on the structure of the network (connections between nodes), not the numerical correlations between node attributes.
Numerical correlation may be useful for building or weighting the network (e.g., in gene co-expression networks), but the hub nodes are identified through network centrality, which focuses on the topological importance of nodes in the network.
The CytoHubba tool in Cytoscape is used to rank nodes in a network based on their centrality or importance according to different algorithms (e.g., degree, betweenness, closeness, etc.). When CytoHubba generates a node ranking, the output is often saved as a CSV file.