 to lecture number six part three if you're watching it on YouTube or if you're watching it later somewhere else like on Twitch. So I wanted to go through like five, six important pathways because they are ubiquitous and or at least in multicellular organisms and they are important because if anything is wrong in these pathways they all deal with primary metabolites. So if anything goes wrong here then you die right because primary metabolites they lead to death if you can produce them. So the first pathway that I wanted to look at is the glycolysis pathway the citric acid cycle and the respiratory chain right so that's what you see here. So the goal of this pathway is to the degradation of glucose to produce ATP so the energy production in the cell. So what happens is we have glucose which is more or less a sugar molecule. This is in glycolysis which is a small pathway in itself is transformed into pyrifat and pyrifat is then the enzyme pyrifat dehydroginase which is just a molecule within the mitochondria makes pyrifat it excrete CO2 and then we get a molecule which is called acetyl-CoA. So acetyl-CoA can be transformed into fatty acids and fatty acids can also be transformed into acetyl-CoA right because the mitochondria can use both sugar as well as fatty acids to power the cell. So acetyl-CoA then is in the citric acid cycle is more or less being reduced and also this process produces CO2 it produces H2 and this H2 is then together with oxygen in the respiratory chain so H2 hydrogen 2 is more or less being burned into H2O and in this process we have an ATP molecule plus PI plus a phosphor molecule which is then transformed into a loaded ATP molecule. The ATP molecules are then transported to where they are needed in the cell and expended when it is required. So it is the process so three steps in the process so going from glucose to pyruvate, pyruvate is then turned into acetyl-CoA. Acetyl-CoA can also be directly obtained from fatty acids and then have the citric acid cycle produces more or less H2 which is not a molecule that can exist but have because of the mitochondria they because two hydrogen atoms can bind together but this H2 molecule then is kind of burned in the respiratory chain using or transforming ADP into ATP which is then used to power all other cellular processes. The next very important pathway is the Hexomonophosphate shunt so this is the degradation of glucose for the regeneration of NADPH so NADPH and ATP are more or less related to each other so what happens is we have glucose 6 phosphate which is transformed into ribulose 5-phosphate which is then transformed into ribose 5-phosphate which can be so it's a it's a circular pathway but it allows the cell to extract energy from RNA and ribonucleotides and this has the ribonucleotides are more or less broken down into ribose 5 which is then transformed into glucose 6-phosphate which then charges NADPH plus into NADPH so it's loading this molecule with an additional hydrogen molecule but it allows for the degradation of glucose to regenerate NADPH from NADPH so spend ATP. We have the glycogen synthesis and degradation pathway which is for the short-term storage of glucose so we have glucose 6-phosphate which is turned into glucose 1-phosphate which then in turn is used by UTP so what happens is that this molecule here so this phosphor molecule with the oxygens is then coupled to each other so it makes a chain so UTP is a carrier which can carry three of these charged phosphate molecules this can then be broken down in pyrophosphate but we can also make udupeic glucose by taking two of these and then adding another sugar molecule to it so this is this is useful because in a cell needs to be able to store enough energy to kind of survive right so if if for a short amount of time no glucose or is is given to the cell then this the cell can actually store glucose as glycogen so it synthesizes glycogen and it can also degrade glycogen again back into glucose so it has a very temporary buffer that it can have to store these energy to store energy not as ATP because the ATP storage is relatively limited but we can store energy as well into glycogen we then have one of the other important pathway which is the gluconeogenase pathway which is the synthesis of glucose from amino acid lactate or acetone and this is one of the more important pathways we again see here the acetylcoide with the pyruvate right so this is this is part which we already saw here right pyruvate to acetylcoide but here what is important is that we have this this circle right which goes so amino acids can be transformed directly into pyruvate so pyruvate can be produced from acetone but also from lactate hey if we have glycerol we can also use that into the acetylcoide cycle where we create ATP and energy production so gluconeogenase is the synthesis of glucose from amino acids lactate or acetone and this is an important pathway for energy production as well so if you want to know more about these pathways right and if you're interested in how certain metabolites are being produced and which proteins or enzymes are involved then go to CAG so CAG stands for the kiosic encyclopedia of genes and genome and it is a database which is full of pathway information so the pathways for example that you can see here this is the glycolysis the gluconeogenase pathway and what you see here is let me see I have a better one so when we look a little bit more in detail then everything in CAG is organized by maps right so you have a map and this map is more or less a combination of metabolites and enzymes so hey in this case when we look we see here alpha D glucose 1p which is then transformed by two enzymes and probably one of these enzymes is enough but there's two different enzymes which can transform D glucose 1 phosphate into alpha D glucose without the phosphate right so enzymes are always listed in square boxes while metabolites are listed as these small little circles and of course you have an arrow which goes from one circle so from one metabolite into the other metabolite and the nice thing about CAG is that it contains pathway information it contains information about the compounds about the reactions and about the genes and the proteins involved in these reactions which means that we can kind of start reasoning about if an animal can produce a certain substance or if it can't right so the MAP pathway is a generalized pathway right so it is not specific to a certain species so if you look at MAP 0 0 1 0 0 which is I think the glycolysis glucogenase pathway then we see the pathway here but then if we select an animal in CAG for example we select horses then we can see that when we look at this pathway that we see that some of the enzymes are colored in green and those are the enzymes which are available to the organism so which are coded into their genome so you can argue now or you can more or less reason that horses cannot turn alpha D glucose 1p into alpha D glucose because they miss the necessary enzyme however they can they can turn alpha D glucose 6p by this arrow into alpha D glucose right so they are able to use this because this protein is there and of course this is really useful especially if you want to make things or if you want to look and make design or bacteria that makes certain substances right because you can see which enzymes are available in a certain species see which ones are missing and especially in bacteria you can easily add these enzymes right you can use a little circle of DNA a DNA vector which encodes the enzyme 3.1 0.3 0.10 right you can click on them and get the name and stuff but they're all of these things are numbered in a in a library kind of system so a kind of Dewey decimal system so have for example horses cannot turn alpha D1 glucose into alpha D glucose with the 1p but they can turn alpha D glucose 6p into alpha glucose if we then look for example at peaches so just a different species we see that peaches actually lack both of the enzymes so they are unable to make alpha D glucose from 1p but also from 6p because they miss both enzymes right so you can see that that every species has a different availability of different molecules so the metabolic pathways are more or less similar between peaches and horses but there are slight differences because not every animal encodes all of the enzymes needed for every step and that is also fine because like you only need to implement part of the pathway because you don't need all of the backup routes that are there right but then very basically if we look at keg we can reason about if a metabolite can be transformed into another metabolite by looking at the availability of the enzymes and the and the map itself is the more or less generalized overview which is not specific to an animal but if we then look at for example horses we see that horses only have a certain amount of molecule or only a certain amount of metabolites but a certain amount of proteins or a certain amount of enzymes to transform the metabolite into another one well for example peaches cannot do this because they lack this metabolite this enzyme so keg is the main entry point for things like pathways or if you're interested in compounds or metabolites it couples these things to genes it gives you an overview of the enzymes but it also has a big drug part so if you're interested in if a certain animal is able to break down cocaine then keg can tell you that right it allows you to reason about which substance an organism produces or could produce under the right circumstances or given the exact input metabolites besides keg there's also the reactome a reactome is very similar to keg but also very different in a way it also contains pathway information it also focuses on many different organisms the nice thing about reactome is that it's open source it also provides many download options so if you want to download right really nice pathway pictures that you want to for example overlay your own data on then reactome can can allow you to do that but the thing about reactome is is that their their overview is much higher right so they they are not looking at individual metabolites like keg does right so metabolite enzyme other metabolite and then this other metabolite enzyme so they are looking at a much much higher level so they have like pathways which are called immune system or they have a pathway which is called reproduction right so they have a much more higher level view of pathways they do allow you to drill down but not to the level of detail that keg does because keg is born more or less from a chemistry background while reactome is more from a molecular biology slash biology background so they have a more kind of global view besides that if you are very interested in the human metabolome database so this is based on the human metabolome project has so this contains all of the information so it it lists all of the different small molecule metabolites that are found into the human body and the nice thing here is is that you can actually search by mass spectrometry profile so if you get a certain mass spectrometry profile then you can just use this profile to search through the database to see if it's a known small molecule metabolite in humans or not so it's a very useful website when you are investigating for example did this person use a certain type of drug because head you can take a little bit of blood throw it into a mass spectrometry get a profile and then using this profile you can search through the human metabolome database to see if a certain drug or a certain thing was used by the sample that you're currently looking at so I wanted to talk a little bit about visualization tools because like keg and reactome they provide the static pictures of pathways right so only when a pathway is known and well studied does it end up being in keg or in reactome but of course when we want to make our own pictures of networks and metabolites or proteins or enzymes and we want to make a kind of a picture ourselves then we can use cytoscape so cytoscape is an open source tool that allows you to visualize complex networks and integrate any type of data so cytoscape is used a lot in bioinformatics but it's also used in social network analysis so for example to visualize your friends right and the friends that are the second circle head so friends of friends or family trees so you can use a lot of things or you can visualize almost anything that you can express as a network using cytoscape so it also allows you to do analysis like semantic web analysis semantic web is the way that on an html page you can have structured data and this structured data can also be visualized as a network graph and so for example you have a person this person has a job and this job is being done at a certain department at this department people are working not just the person that that is the current one and so it allows you to build up these really nice pictures about anything that you can more or less visualize in a 3d network so it is a really useful and handy tool so I just wanted to show you guys some some things that you can do with it so one of the things is that when you look at cytoscape and you start it up this is a really older version then you get this welcome overview and then you have several options to get access to these metabolic networks right so you can just give it your own network file so you can just make your own network file and then use that to visualize it but you also have access to all of the big databases so hey if I want to for example look at certain pathways in in say elegans or in humans and then by clicking these buttons you can directly download the whole metabolic pathway for for example gluconeogenesis in humans so for example if we use a network file then there are certain things that we can do with it because cytoscape has a lot of options to to change the visualization so how we can go to the layout so layout allows you to change the layout and if we do that then in the control panel we get a network a style and a select so in the style tab within the control panel you can change the style of the network and you can for example highlight certain things or you can make that arrows look little look different from what they look before so how do I use that so if I click on the style tab right so a network is connected of nodes and edges right so a node is more or less a thing and an edge is something that connects it right so a node can for example be a person and an edge can for example be a relationship of this person so you can have many different types of edges right because a person has a father it has a mother but he can also have friends and he can have a family right or they people can know each other very superficially the same thing holds for these nodes right because nodes can also consist of different types right so we can have different types of nodes and we can color them and highlight them in different ways so how do we do that well we have the style tab so when we click the style tab on the bottom we see here node edge and network so node defines how nodes look like so we can for example set the fill color of a node to a defined color but we can also use a mapping which means that based on the type of node if it is a person we can color it blue but if the node is for example a location we can color it yellow right so you can make you can visualize literally anything that you can think of using cytoscape and how to do this well you can use the style tab and in the style tab you can set all of these things like how do I want a node to look like and do I want that look to change based on the type of the node or other node information the same thing holds for edges and the same thing holds for networks or network holds kind of global settings look what is the background color of the network but the the edges can also be like do I want to have an arrow do I want to have a double arrow do I just want to have a line do I want to have a dotted edge so nodes are the kind of main hubs and edges connect nodes together so the nice thing about cytoscape is that it has more or less the easiest input format ever because everything that is being inputted in cytoscape consists so the network itself consists of a three a three column matrix right so we have the name of the first node then we have a top so a tab character then we have an edge and then we have another top and then we have another name of a node right so if I would write down node one top edge no top node two no two top edge top node three and I would load it into cytoscape and cytoscape would visualize it like this right so node one is connected to node two node two is connected to node three if I wanted node one to connect to node three I would just change node two here to node three and then this arrow would not point to this but it would point to there right it's it's really the easiest input format ever so it's a it's a how do you call it it's kind of a like a no SQL database so it's a it's it's just a three column format so it's it's from so it's it's goes from the the origin relationship target origin relationship target good so I don't want to talk that much more about cytoscape because I think there is an assignment about you guys just using cytoscape if you guys want and I have cytoscape installed I can actually probably show you some cytoscape magic and in how you want to do that I haven't set that up and like I said last time you should never do a live demo or something like that but if you guys want then actually I can I can just show you a little bit of cytoscape and cytoscape is really really handy right so if in the in the future you need to visualize some kind of a network then you can use cytoscape for that all right so let me then just set up cytoscape right and add a new just a little view yeah and that's not an issue so we still have like 25 minutes left so let me do a window capture and then here we have the window capture for cytoscape so this is cytoscape in live right so when you open it up and I already clicked on okay wait a second that's that's way too wide all right so let me do it like this right so this is this is cytoscape and the way that it looks so first we need to have an input file right so I'm just going to create a very basic input file like the one that we had so let me show you guys notepad plus plus and then of course cytoscape needs to go to the back so I'm just going to create an input file so I'm going to say Denny then I need to have a top character which I actually don't have so let me see if I have a top character anywhere loves Oscar all right Oscar loves food apples are yeah this food for Oscar that is a good one so that means Oscar eats right something like that right so had just building up a network so we have a node a relationship and then another node and then we have Oscar so have we can just build up a network so let's save this network somewhere so I'm just gonna save it on the D drive so I'm just gonna call this network test I don't know if you need a specific extension alright so let's go back to cytoscape and then inside escape we're just going to say file and you guys can see cytoscape so and we're just going to say file and then we're going to say open and then let's see if it opens up the basic network here network test open it up and then it says that it cannot open it because we just say no we want to import a network from a table right so we are going to select our input type and then we're just going to say network dot test we're going to open it up and then we're going to say the source is in column one the interaction is in column two and then the target is in column three oh you guys can see that that's so horrible that I can't capture the overlays let me make a screenshot for you guys so just so that you guys can see what I'm seeing so this don't save do it like that I'm just going to show you the paint window that's one of the drawbacks of so when you when you click on network from file then you get a picture which looks like this right so I just say well load in the network test the interaction the source of the interaction is in column one the interaction type is in column two and the target interaction is in column three and then it will say here that columns in blue will be loaded as edge attributes so if I want to add additional attributes to every edge then it can add it as additional columns right but let's just go back to cytoscape all right so when we go back to cytoscape and I just press import all right then it imported it successfully so it shows me that this is the kind of network that it creates right so food is central then we have hoop we have oscar and we have denny right and now I can go to the style tab and I can start modifying it so I can just say layout no I can go to vizmapper so they renamed it to vizmapper and then I can just take one of the pre-existing network styles like why doesn't it apply that doesn't matter so first things first we want to color the edges right so the edges we want to have different edges for the types that we just defined because we have love oh loves sorry we have love we have are we have eats and we have these kinds of things yes so that's what we're going to do right so we're going to change the the edge line color edge line style we can double click and now we have a mapping on the edge line style and I want to say well the interaction I want to do have a discrete mapping why does it based on the ID let me see it's been a little while and this version hey is this not edge line style this on this all right I'm just going to create a new visual visual style just call it something right so now we have an empty visual style and now we can start styling it so the edge line style I want to based on the mapping type I want to have a pass through a discrete mapper let me see that attribute browser why does the edges not have an ID why are the colors also not there edge label call no I don't want to have the edge of this mapper thing edges this mapper yeah if my face mapper open so now let me see let me actually say that the so I want to first show the nodes and I want to show the node names so not the border color not the font size the label color position with is that oh why does it not allow me to do because the edges don't seem to have IDs so I'm a little bit confused why it doesn't show me any because normally when you select one of these then it should be all right so you guys can see that again because there's again like a pop-up that pops up why is that not showing I think it has everything on white or something I don't want to import let me let me try this again so I'm going to import my network from a table I'm going to import the file that I just made all right and then I'm going to say column 1 column 2 column 3 import all right so then we get this network when we have this network we can then apply it actually doesn't even apply the visual style at all delete visual style yes all right so now we're back to the default style and now what I want to do is I want to change stuff so I want to change the node shape into a triangle apply apply yes so that works oh this is just a browser this is so useful I'm sorry I'm bumbling around a lot but the weird thing is is that I can only change the like this thing here the default so when I click on it I get a pop-up but you guys can't see the pop-up which is just annoying as hell let me do it slightly differently because I am just going to capture the whole screen so I'm just going to do not a window capture but a display capture so this is the whole thing that's good then you guys can see my screen which is fine and then let me just put that thing close down all of the other windows so we know more or less what we're doing and then this one can go as well this one can go all right so you guys can't see me now but that's okay all right so we're we're here right so let me open up side to escape a little bit so when I click here now you see the pop-up right and now I can say nodes so I want to have the but I don't want to change the default properties I actually want to change the properties here and I want to just use a discrete mapper and normally it would now show me all of the options that I have but it doesn't give me any way and if I select an edge it also doesn't show me the IDs of the edges which it normally would be like because if I would select this one then it should show me ID is food canonical name is food for some reason it doesn't you know I destroy the whole network queue go to network file import network from a file select the file that I want source column three import now I want to go to this mapper it still doesn't load in the attributes I can add attributes probably manually but why does it not try this so I want to load attributes select file select my network mapping options no is space separated column one key attributes I have no idea why this doesn't work at all no idea no idea guys so I will do a demo next time I will figure out why this thing doesn't do what I want to do not going to figure it out live on streaming there's probably some basic step that I'm missing which is just the way that it is it also didn't look the way that I expected it to look when I opened it up it might be that I just have to install it but it's it's weird because normally what you would have is that you would have a style tab but it doesn't give me the style it just has this vizmapper tool and this vizmapper tool just doesn't allow me to create any pass through mappings or canonical names or anything and it also when I select the nodes normally it would show the different attributes for each node it used to be very simple tool but since site escape has been updated to version like actually like 600 versions behind let me actually see what oh the current version is 3.8 and I'm trying 2.7 so that's actually not a all right let me I'm just gonna try it again we still have like 10 minutes left to the end of the lecture so I'm just gonna reinstall it see if that will fix anything because they used to use it a lot and it's a really good tool for visualizing networks but the problem with tools is that if they're good tools all right and now I get the Microsoft has protected your pc so annoying so annoying so you go to properties and then you say unblock and you press apply and then you can install it oh and now I have to install the correct java version as well this is so nice all right because I didn't prepare it right and I just made the slides like four years ago when I was using a completely different version but uh that's just the way it is like never do a live demo right that's uh that's what people always say so doing a live demo is a bad thing if there's any questions just throw them in chat as long as the question is not um how do you do this how do you uh how do you use site escape other questions are more than welcome um that one as well I am installing site escape at the moment so um just to see if the new version will be easier for me to show you guys yeah my my the current version that I'm installing is also 3.9 though so just having to wait a little bit let me actually move this to the question slide so that you guys can ask a question if you want to I actually didn't even include a question slide so let's just finish at the overview slide then right so during the lecture I told you about metabolites right primary metabolites are things which are required for being alive secondary metabolites it's okay if you don't have them right you don't die directly I told you a little bit about mass spectrometry that it comes into four different steps I mentioned three are here the first step is compound separation using chromatography or electrophoresis furthermore I'm doing fragment you're doing fragmentation and ionization the last step in mass spectrometry is doing separation by mass over charge furthermore I showed you three different databases which allow you to deal with metabolites so if you have mass spectrometry data you can use the metlin database to identify the components inside of the spectrum furthermore I talked about the keg database which is a database which shows metabolites and enzymes working on these metabolites and which allows you to reason if a certain animal can produce a certain metabolite but is also very useful if you do bacterial modification right to have a bacteria make a very specific component that you want furthermore I told you about reactom which is very similar to keg but has a much higher level overview and I told you a little bit about visualization and try to do a demo of cytoscape which unfortunately did not work but we will do one at the beginning of the lecture next week so for me that's everything if you have any questions let me know I will set up cytoscape and give you guys a demo next week since it's almost four so that's everything for today good so if there's no question then I will see you guys next week and thank you guys for staying here there's six people left so that's good so thank you all for being here and see you guys next week