Sir as a food technology student are there any tools that I could be using , please dig some works that can link bioinformatics in research field of food science....it would be a huge help sir...I am a noob in bioinformatics but want to learn so that I can use it for Thesis purpose,you seems like a light in the dark to me ... please guide sir
@@divz2646 The obvious things that come to mind with respect to using Cytoscape and stringApp are the compound query and PubMed query. The compound query allows you to query STITCH for a chemical compound, including vitamins and microntrients, and obtain a network of the associated proteins. The PubMed query allows you to query the literature for anything that you can query PubMed for (e.g. food-related terms), analyze the matching papers for which genes/proteins are mentioned, and then retrieve a network.
Hello Professor, for the enrichment analysis from a cluster generated from an unclustered network by mcl clustering, can I use the genome as the background instead of the unclustered network?
You can but the results would be different. If you use the whole genome as a background, you may find some terms that are overrepresented in almost all clusters, because they are simply enriched in the network in general. That's why I prefer to do two separate enrichment analyses: one that compares the whole network vs. the genome to find out what is generally overrepresented, and another that compares each cluster to the network to find out what is special about each cluster.
@@larsjuhljensen i want to analyse wheat. i have another question sir, how i can analyse my compound's effect on polymorphic genes using cytoscape? please guide me sir. i know how to assess on disease genes. but want to know how to assess effect on polymorphic genes.
Hi Prof. Jensen. Thank you for sharing your knowledge free. Grateful to you. Could I request another great video if possible. It would be great if you make a video lesson on mass spectrometry-based phosphoproteomics. I see you are an expert on this subject. So Could you give us an introductory workflow from protein isolation to bioinformatics data analysis workflow behind the phosphoproteomics techniques? Looking forward to hearing from you.
Glad you liked the video! I am certainly thinking of making more lessons, ideally in the form of shorter videos on more specific topics rather than large monolithic lectures. I'm not 100% sure if I'm the right person to cover the full topic that you mention, though. I'm not an expert on mass spectrometry, but maybe what is needed is indeed a primer on the topic as opposed to a more in-depth technical description.
@@larsjuhljensen Thank you Prof. You may skip the machine part. I am much more interested in how data analysis performed and downstream data analysis. I see many transcriptomics RUclips lessons, however no handful of proteomics vidoes. Your contribution would be greatly appreciated by the worldwide students/researchers.
Dear Professor, very nice video for Network analysis given by you. By the way, I hereby found a Postdoc position vacant in your lab, however its too late. With my curiosity I am eager to know and join in your lab based on your favour reply. Thanking you, looking forward to hearing from you if any Postdoc vacant available.
I'm sure there will be other positions opening in the future. However, it will probably be a little while since I have several new people starting in the group right around now.
For those asking about training material: have a look at the stringApp and Omics Visualizer tutorials at jensenlab.org/training/
Sir as a food technology student are there any tools that I could be using , please dig some works that can link bioinformatics in research field of food science....it would be a huge help sir...I am a noob in bioinformatics but want to learn so that I can use it for Thesis purpose,you seems like a light in the dark to me ... please guide sir
@@divz2646 The obvious things that come to mind with respect to using Cytoscape and stringApp are the compound query and PubMed query. The compound query allows you to query STITCH for a chemical compound, including vitamins and microntrients, and obtain a network of the associated proteins. The PubMed query allows you to query the literature for anything that you can query PubMed for (e.g. food-related terms), analyze the matching papers for which genes/proteins are mentioned, and then retrieve a network.
@@larsjuhljensen Thank You!❣️🙏
Thank you.
Hello Professor, for the enrichment analysis from a cluster generated from an unclustered network by mcl clustering, can I use the genome as the background instead of the unclustered network?
You can but the results would be different. If you use the whole genome as a background, you may find some terms that are overrepresented in almost all clusters, because they are simply enriched in the network in general. That's why I prefer to do two separate enrichment analyses: one that compares the whole network vs. the genome to find out what is generally overrepresented, and another that compares each cluster to the network to find out what is special about each cluster.
Thank you for the reply
How to use cytoscape for nutrigenomics. I want to understand links of wheat with proteins, metabolic pathways and diseases. Please guide me sir
What would be the data that you want to start from? Is it wheat or human proteins you want in the network?
@@larsjuhljensen i want to analyse wheat. i have another question sir, how i can analyse my compound's effect on polymorphic genes using cytoscape? please guide me sir. i know how to assess on disease genes. but want to know how to assess effect on polymorphic genes.
Hi Prof. Jensen. Thank you for sharing your knowledge free. Grateful to you. Could I request another great video if possible. It would be great if you make a video lesson on mass spectrometry-based phosphoproteomics. I see you are an expert on this subject. So Could you give us an introductory workflow from protein isolation to bioinformatics data analysis workflow behind the phosphoproteomics techniques? Looking forward to hearing from you.
Glad you liked the video! I am certainly thinking of making more lessons, ideally in the form of shorter videos on more specific topics rather than large monolithic lectures. I'm not 100% sure if I'm the right person to cover the full topic that you mention, though. I'm not an expert on mass spectrometry, but maybe what is needed is indeed a primer on the topic as opposed to a more in-depth technical description.
@@larsjuhljensen Thank you Prof. You may skip the machine part. I am much more interested in how data analysis performed and downstream data analysis. I see many transcriptomics RUclips lessons, however no handful of proteomics vidoes. Your contribution would be greatly appreciated by the worldwide students/researchers.
Dear Professor, very nice video for Network analysis given by you. By the way, I hereby found a Postdoc position vacant in your lab, however its too late. With my curiosity I am eager to know and join in your lab based on your favour reply. Thanking you, looking forward to hearing from you if any Postdoc vacant available.
I'm sure there will be other positions opening in the future. However, it will probably be a little while since I have several new people starting in the group right around now.