Thank you very much for the video and video starts at 24:30
@shbangash437 Жыл бұрын
Incredible. This video clear all my concept . I really appreciate 🙏 your effort sir . Thanks for this session on KZbin .
@larsjuhljensen Жыл бұрын
Happy to hear that! :-)
@Biomeducated3 жыл бұрын
24:45 START + INTRO + TOPICS in this webinar 33:47 STRING DATABASE and its features 47:51 How are various databases integrated in STRING? (Physical interactions, Co-expression data, etc.) 59:20 Break 1 (5 min) - Q's answered from chat box 1:04:22 How are various databases integrated in STRING continued. - Specific zoom in on 'Text Mining' from LITERATURE! 1:12:45 Knowledge Graphs - How all this mapped data is visualized 1:16:19 Answering questions 1:41:20 Overview of the web-based EXERCISES + Questions 2:01:55 EXERCISE 1 explanation 2:10:26 CYTOSCAPE visualization of STRING data 2:22:18 Use clustering (ClusterMaker2 app) for better interpretation of the network 2:22:58 SUMMARY + Acknowledgements 2:28:23 Example to interrogate PubMed for 'antibiotic resistance in S. pyogenes' in CytoScape + Network customization 2:35:25 Tutorial with Spreadsheet to Network 2:41:10 How to combine 2 networks? 2:46:40 Use of ClusterMaker2 2:50:12 Quest for questions 2:55:30 Mapping of compounds to proteins 3:08:17 Close-off *Thank you so so much for sharing this, Prof. Jensen!* Sharing stuff like this will accelerate scientific (and drug) discovery. I'm going to dive into my RNA-seq DEG lists with this new knowledge RIGHT NOW! So excited!
@larsjuhljensen3 жыл бұрын
Thank you!
@rufel93323 жыл бұрын
Thank you so muchhh
@larsjuhljensen3 жыл бұрын
You're very welcome, I hope it was useful!
@jairsoto61502 жыл бұрын
Chingón, carnal. Gracias por compartir tu experiencia, me ha sido de mucha ayuda.
@larsjuhljensen2 жыл бұрын
Glad it was helpful :-)
@Saed76303 жыл бұрын
Very informative talk/presentation!
@robertofernandorosalesroja53803 жыл бұрын
Great demo, awesome talk!!!! Thanks!
@larsjuhljensen3 жыл бұрын
Thank you very much - glad you liked it!
@TheManiaKyu3 жыл бұрын
demo work really helped a lot. thank you very much~
@supatkhongfak80222 жыл бұрын
Thank you very very much
@larsjuhljensen2 жыл бұрын
You are most welcome!
@antonyshadowbanned2 жыл бұрын
Brilliant presentations, thank you so much
@larsjuhljensen2 жыл бұрын
Glad you like them!
@nidhidubey47989 ай бұрын
sir, if i have a set of genes with me. Can I make a gene regulatory network using cytoscape?
@larsjuhljensen9 ай бұрын
Yes and no. Cytoscape is a tool for analysis of networks and visualization of them, so Cytoscape itself is not going to make any any kind of network from a set of genes. However, if you have a source of regulatory interactions for your genes, you can easily import those into Cytoscape and visualize it (and it is a very good tool for that). Also, we are working on adding regulatory interactions to STRING, so in the future you will be able to import obtain a regulatory network in Cytoscape by using stringApp.
@masoudrezaei3313 жыл бұрын
this video was awesome! wish you the best professor!
@larsjuhljensen3 жыл бұрын
Thanks!
@KainBAl3 жыл бұрын
Thanks Sir. This video has been very educational for me, I am very new to using these tools. I have a question, once I have my network in cytoscape and I have different groups of proteins separated into clusters, how can I assign a specific biological function to each of these clusters.
@larsjuhljensen3 жыл бұрын
What you can do is to select all proteins in one cluster and then run the stringApp enrichment analysis on the selection only, using the full network as the statistical background. That will give you enriched terms for the selected cluster. It's bit of a faff, but you can obviously repeat this for all of the clusters, one at a time. I wish there was a way to automatically do it for all clusters, but that is not presently possible.
@meenalbhardwaj48833 жыл бұрын
is there any upcoming webinar for Cytoscape, string, ClueGo, MCODE I want to learn this tool for my master's project. the session should include live interaction if possible
@larsjuhljensen3 жыл бұрын
I have already recorded a brief introduction to Cytoscape, which I plan to publish either Friday this week or Monday next week. I do not plan to cover ClueGo specifically, since I do not use it myself, but I will be covering enrichment analysis. Also, I intend to make a presentation about network visualization, which should include both network layout and network clustering (although likely not MCODE specifically). For a practical part, I recommend that you take a look at the online exercises at jensenlab.org/training/stringapp/
@sachinsahu533 Жыл бұрын
How to prepare the Protein-Protein Interaction network, and which software is used to prepare for the network.
@larsjuhljensen Жыл бұрын
I'm not sure what network you want to prepare. As described in the presentation, you can get a network for a set of proteins from STRING. Not sure what you mean by "prepare", since these networks already exist. But if you want to analyze the networks, Cytoscape would be the tool of choice.
@sachinsahu533 Жыл бұрын
@@larsjuhljensen Thank you Sir
@mamoketebokhale62833 жыл бұрын
Hi Prof Jensen, I had an input of 30 proteins (upregulated genes) and got only 3 interactions ( out of 15 items of the output) on STRING, in this case do i expand and add more interactors on the shell? Is it also advisable to hide disconnected nodes
@mamoketebokhale62833 жыл бұрын
That is when i used high confidence (0.07)
@larsjuhljensen3 жыл бұрын
If you started with 30 proteins and got only 15 in your network to start with, it sounds like you have had some issues with the names you used for searching. That would be the first thing that I would check. Regarding number of interactions, which organism are you working on? The density of the network varies greatly between organisms; in some 0.7 may be a quite high confidence cutoff to use.
@mamoketebokhale62833 жыл бұрын
@@larsjuhljensen Thank you so much Prof, i mentioned on one of your videos that I work with Pectobacterium. You are very correct it seems for some of the names it didnt recognise them. I would do further searches on the names.
@shahabmirshahvaladi62393 жыл бұрын
great tak
@shahabmirshahvaladi62393 жыл бұрын
i wish the string viruses database included COVID proteins as well, comes real handy these days!
@lichuinchong61614 жыл бұрын
For STRING network analysis, what is the difference between two clustering algos, k-mean and MCL? bcoz both are giving me different results, which one should I follow and/or better?
@larsjuhljensen4 жыл бұрын
In my experience, MCL is the better algorithm for clustering networks. From a user perspective, the big difference is that you explicitly say how many clusters there should be when using k-means. Unless you choose that number wisely, k-means will give poor results.
@vrundakumbhar56514 жыл бұрын
Sir can you please leave the exercise link here on KZbin? Please please please 🙏
@larsjuhljensen4 жыл бұрын
All exercises can be found at jensenlab.org/training/
@vrundakumbhar56514 жыл бұрын
Sir you have said a proteomic experiment and data is arrived from that... So I want to ask if we want some proteomic data can we get it direct without any experiment directly from proteomic databases?
@larsjuhljensen4 жыл бұрын
Most often tables like this are available as supplementary information files in proteomics publications.
@elisabettaversace9323 жыл бұрын
brilliant, thanks! As a novice, I would have 2 questions 1) when are high/medium/low interactions scores recommended? maybe there is a publication that explains this and I did not find it. If I have just 50 genes that come from the same experiment, shall I use medium or low of high? And I guess I should use the same criterion for different conditions/experiments in the same work, right? 2) shall I prioritise evidence from experiments in the interaction sources? I thought that maybe data mining can inflate some associations reporting what is already known multiple times, but maybe this is accounted for. What is the gold standard? Maybe there is an obvious paper as a reference for this... Thanks a lot
@larsjuhljensen3 жыл бұрын
There is no simple answer to which confidence cutoff to use - it depends on a lot of things, including what you're trying to accomplish, how many genes you're looking at, and how well studied they are. For visualization purposes, it will always be a pragmatic choice: if the interactions that are actually interesting to you are all high confidence, you're probably best off not showing a lot of lower confidence interactions that just muddy the message. And yes, I would certainly not want to mix and match different cutoffs within one analysis. If, on the other hand, you are using the network as input for an analysis like clustering, I would almost always want to include all interactions even with the lowest confidence, but of course take the confidence scores appropriately into account in the analysis. The reason is that throwing away part of your data before even starting is rarely a wise choice.
@larsjuhljensen3 жыл бұрын
If what you want is a functional association network, then the weighting of evidence is already inherently done. Since all evidence sources were benchmarked on pathway knowledge (from the KEGG database), the confidence scores already weight them correctly. There are cases when you would want to exclude some types of evidence, usually to avoid circular reasoning in downstream analysis. But I cannot think of a situation when I would want to use all of them but prioritize them differently. Not unless what you want is in fact a physical interaction network, but we now give you the option to have that instead of functional associations.
@gayathrisudarsan90444 жыл бұрын
I have one question regarding STRING. I have around 400 targets for which I need to collect only the pathways. When I try to input using the multiple proteins options, it forms a network of 256 proteins and I get around 137 pathways. What I need is the pathways for each target from the list of 400 and odd targets and it's fine if there are overlaps as I wish to construct a network using that. Is there a way of doing it?
@larsjuhljensen3 жыл бұрын
If you go to the "Save / Export" section at the bottom of the "Analysis" page, you can save the enrichment results. It contains a column with the matching proteins for each term/pathway, thus allowing you to get the information you are requesting.
@gayathrisudarsan90443 жыл бұрын
@@larsjuhljensen I tried that and I got the results for all the 427 genes I had. Thank you!
@chigurupalliraja19092 жыл бұрын
hi sir, i am searching for protein-ligand interactions for cancer in cytoscape which is my project.. ex: protein is 1TUP and ligands are some lets say 10. i should use this cytoscape software and find best ITUP - 10 ligands. so if ligand1 is better for ITUP protein so the answer is ligand1. please help me regarding this
@chigurupalliraja19092 жыл бұрын
and my main work is finding targets for proteins so....importing proteins in one column and ligands in second column and importing them in cytoscape is fine but i am having doubt regarding how should i write those protien and ligand names in that excel sheet so that cytoscape can understand for example i have protein 1TUP and ligand as alpha pinene how should i write these in those columns sir please help me regarding this thank you sir
@larsjuhljensen2 жыл бұрын
Here's the thing: Cytoscape doesn't know anything about proteins or ligands. So the names that you use only matter if you need to merge in other data, in which case you want to coordinate the names across whichever data sources you need to combine.
@johirislam81743 жыл бұрын
Hi i analyzed my PPI netwrok by clustalviz which is cytoscape plugin.Here the results came by rank.So now i am confused which one i should pick
@larsjuhljensen3 жыл бұрын
Sorry, I don't understand your question. I'm not familiar with clustalviz.
@ahmedhashim57833 жыл бұрын
When I upload a table from File to visualize the netowrk, the columns appear blank and empty of content. I tried several file,, txt, xml, csv... and installed previous versions of Cytoscape, but the problem was not resolved!
@larsjuhljensen3 жыл бұрын
I'm almost certain that your problem is that the column you selected as "key column" in the file you import does not match what is in the column you selected as "Key Column for Network". If the two do not match, none of the nodes in your network will match a row in the table that you're importing, and the result will be precisely what you describe: the new columns are created but they are all empty.
@ahmedhashim57833 жыл бұрын
@@larsjuhljensen The list of genes that I entered into String protein query is 5100, 4600 genes passed filter and the network was formed. The same excel sheet from which I took the gene list I used it as a table to visualize the network, (the goal is to visualize the upregulated and downregulated genes), the excel sheet contains in addition to the gene id column, some columns like fold change, p.value.. etc. When I emport the table, the key column is gene id with the shered name column in the network. The result; columns display only their titles but are empty
@larsjuhljensen3 жыл бұрын
@@ahmedhashim5783 If you used stringApp to retrieve the STRING network, the gene ids from your Excel sheet will not be in the "shared name" column of the network. That column will instead contain the STRING protein ids. The terms you queried with (i.e. gene ids in your case) will be in the column called "query term". You can find a detailed explanation of this under jensenlab.org/training/stringapp/#33-data-import
@ahmedhashim57833 жыл бұрын
@@larsjuhljensen Exactly, I had do this yesterday and was succeeded. Thank you
@zhanyouxu83254 жыл бұрын
Thank you very much for the video. I have one question as below: When I tried to import network from public databases, under "data source:" I can see ONLY one option: universal interaction database client. I can NOT see other data sources. How can I add/see other data sources? Thank you.
@larsjuhljensen4 жыл бұрын
You need to install stringApp from the Cytoscape app store to make the other options appear.
@zhanyouxu83254 жыл бұрын
I figured it out that I need to install the stringapp. thanks.
@shashishekharsingh26854 жыл бұрын
which file should i download from string to make PPI in cytoscape?? Please reply
@larsjuhljensen4 жыл бұрын
No need to download any file. Just install stringApp from the Cytoscape app store. See exercises at jensenlab.org/training/stringapp/
@stephanyroserorojas8944 жыл бұрын
HOW DO I INCREASE THE NAMES OF THE KEGG ROADS TO MY INTERACTION NETWORK? THANK YOU
@larsjuhljensen4 жыл бұрын
Not sure what you mean, sorry.
@shadyamr97754 жыл бұрын
Hello, thanks a lot for the introduction. I have a question I tried to import the "antibiotic resistance streptococcus " as you did but it give an error and doesn't work?!
@larsjuhljensen4 жыл бұрын
I cannot guess why that would be. I just tested and it still works fine for me.
@shashishekharsingh26854 жыл бұрын
How do i link proteome network to transcriptome data? if you can make video on that that will be very helpful.
@larsjuhljensen4 жыл бұрын
If you have a list of differentially expressed genes that you want to map to a protein network, you'd do it exactly the same way as for a proteomics dataset: jensenlab.org/training/stringapp/#exercise-3
@بلالجاسر-ج9ذ4 жыл бұрын
Hello dear Sir Thank you very much for the nice explanation Sir, may I get your help to build up my network then choose the most active protein for a specific disease?
@larsjuhljensen4 жыл бұрын
It is not really clear to me what you mean by "most active" in this context.
@بلالجاسر-ج9ذ4 жыл бұрын
How can I recognize the proteins to do docking from the results of cytoscape or string??
@biogerontology76464 жыл бұрын
55:00
@bidwansekhar2 жыл бұрын
Take me as a PhD then
@larsjuhljensen2 жыл бұрын
Sorry, I don't currently have open PhD position. But I advertise all positions at jensenlab.org/, and they are filled in open competition. I often have one or more strong candidates that I know will apply, but I always tell them that there is no guarantee they will get it. So feel free to apply when I advertise a position :-)