PathRings. Manual. Version 1.0. Yongnan Zhu December 16,

Transcription

1 PathRings Version 1.0 Manual Yongnan Zhu Deember 16,

2 PathRings This tutorial introdues PathRings, the user interfae and the interation. For better to learn, you will need to refer to the sreenshots in this doument. You will learn: How pathways are visualized in PathRings How to overlay orthologous data on pathways How to overlay expression data on pathways How to interat with our tool You will learn:... 2 What is this tutorial For? Full Sreen mode Menu of the sene Menu of the Bubble Supporting Pathway network format Supporting Pathway ortholog gene data format Supporting Pathway gene expression data format Cross-talking Information Ortholog Analysis Gene Expression Analysis Contribution to this tutorial: Yongnan Zhu, Liang Sun - 2 -

3 What is PathRings? PathRings is a web-based appliation of biologial pathway visualization and analysis, allowing users to visualize, searh pathways from Reatome, to upload their own gene orthologous data for ortholog analysis, and to upload their gene expression data for expression analysis. This is a web-version of PathBubbles projet: The urrent version is 1.0. It ould be run on any PCs (both Linus, Windows, Ma OS). Please use Chrome to use our tool. It is freely available at (see Figure 1). All the ode is hosted on Github, you an fork it through the link: We submit a paper to Bioinfomatis, if you would like to do analysis based on this tool, please quote the referene below. Yongnan Zhu, Liang Sun, Carl Shmidt, Keqin Wu, Zhigeng Pan, Jinglong Fang, J. C. PathRings: an web-based tool for Exploration of Ortholog and Expression Data in Biologial Pathways[J] (submitted to BMC Bioinfomatis). Figure 1. Homepage interfae What is this tutorial For? This tutorial introdues features of PathRings using a ombination of short explanations and examples. You will learn how to interat with PathRings, how to visualize pathways, how to do orthologous relationship analysis between two speies, how to do expression data analysis and if neessary, you an ontat us for help

4 1 Overview f a d e b Figure 2. An overview of PathRings interfae (a) Virtual working spae: a panning bar to show an overview sene; (b) A large working spae with lots of bubbles, inluding () Sunburst visualization bubble; (d) Sortable table bubble; (e) Query symbol from NCBI; (f) Current viewpoint to show the bubbles of urrent working spae PathRings supports data exploration of four types of pathway relationships, whih inludes hierarhial relationships, ross-talking relationships, orthologous relationships, gene expression relationships. In PathRings, we treat eah funtional view whih is used to reate and present visualization as a metaphor of Bubble. Bubble an be grouped and ungroup. Figure 2. provides an overview of the PathRings interfae. (a) is the virtual working spae whih is a panning bar to show the overview of the urrent bubbles in the sene with a shrunken view. (b) is a large working spae (we will all it sene in this tutorial), whih is used to present the urrent visualization bubbles. () is a Sunburst visualization of all the human pathways whih overlays expression data. (d) is a table to show the detailed information of gene produts. (e) is an information view to obtain the gene information for NCBI browser

5 1.1 Operation Menu Full Sreen mode You an press F/f on your keyboard to swith to full sreen mode. If it is on the Full sreen mode, you an press Es on your keyboard to exit the Full sreen mode Menu of the sene In PathRings, if you right lik on the sene, it will pop out a menu. (see Figure 3). You an view individual pathway network graph by selet Open Pathway Graph menu, it will add a Graph Bubble on the sene. You an view all the pathways in a tree-ring by selet Open Pathway TreeRing menu. It will add a TreeRing bubble on the sene. You an view the simple tutorial by selet Open Simple Tutorial and you an delete all the bubbles on the sene by selet Delete All. Figure 3 ontext menu on the sene Menu of the Bubble In PathRings, all the bubbles an be group and ungrouped, and also they an be deleted. Every Bubble (Figure 4 (a), (b), ()) has a menu on the right orner with three buttons whose labels are (U/G, X, M). For the U button, this means the urrent bubble an be group (if it is overlap another bubble, they an be grouped), and if the U button beomes G tag, it means this bubble an t be grouped (if it is overlap another bubble, they an t be grouped). X means lose the urrent bubble, you an delete the bubble from the sene just by liking X button. M means funtional menu for this bubble. (Only Graph Bubble and Tree-Ring Bubble have this menu). In addition, there is an additional R button for Tree-Ring Bubble, if you zoom in the tree-ring, you an lik R button to reset the tree-ring to the default zoom level. There are three types of bubbles ould be added onto the sene: Pathway Graph Bubble (Figure 4 (a)), Pathway TreeRing Bubble (or Sunburst, we all tree ring here) (Figure 4 (b)), Table Bubble (Figure 4 ()). You an open Pathway Graph Bubble (Figure 4 (a)) and Pathway TreeRing Bubble (Figure 4 (b)) by seleting the ontext menu on the sene. Table Bubble (Figure 4 ()) is seleted from Pathway TreeRing Bubble. (Detailed desription will be introdued in setions below)

6 b a Figure 4 Desription of three types of bubbles: (a) Pathway Graph Bubble, (b) Tree Ring Bubble () Sortable Table Bubble (1) Pathway graph Bubble You an view an individual pathway network graph by selet Open Pathway Graph on the menu of sene. It will show you the default empty Bubble view (see Figure 5 (a)). And then you an lik M button to open the funtional menu (see Figure 5 (b)) on the right orner of the Bubble, you an hoose the pathway network data to view the individual network graph (see Figure 5 ()). a b Figure 5 Viewing pathway graph: (a) Empty graph bubble (b) Menu of graph bubble () Load ABCA transporters in lipid homeostadis.xml pathway data (2) Pathway Tree Ring Bubble You an view all the pathways (1417 from Reatome) in a tree-ring by selet Open Pathway TreeRing menu on the sene. It will show you the default view. (see Figure 6) On the left top orner of the bubble (Figure 6 (a)) is a label to show you the orthologous speies or the name of your urrent input data file. On the right top orner of the Bubble (Figure 6 (b)) is a olor mapping to show you the enoding in the ring. (Figure 6 ()) is the menu of the tree-ring. Through this, you an hange the orthologous speies or input your orthologous table

7 a b Figure 6 Tree Ring Bubble graph: (a) Label to show the input orthologous data (b) Legend to show the olor mapping () Menu bar of Tree Ring Bubble (3) Pathway Table Bubble You an view the detailed protein information by right lik the bar (Figure 7 (a)) or right lik the ar of eah pathway on the TreeRing Bubble View. It will add a bubble (Figure 7 (b) ). From Table, if you are interested in a speify symbol, you an right lik it, and it will add a Table Bubble with detailed protein information of this symbol (Figure 7 ()). b a Figure 7 view detailed protein information through Table bubble

8 1.2 Input Data Format Supporting Pathway network format The pathway graph in Pathbubbles supports pre-defined XML format. We will first show you the sample example, and then tell you the detailed format. Table 1. XML file Format <?xml version="1.0" enoding="utf-8"?> <Pathway> <ompartmentblok Num="3"> <ompartment j="0"> <Name>early endosome membrane</name> <Position>( , , , )</Position> <Contain>(C,1,;S,1,;S,14,;S,4,;S,6,;S,8,;S,9,;S,15,;S,16,;S,19,;S,20,;S,24,;S,26,;S,29,;S,30,;S,34,;S,36,;R,1,;R,2,;R,3,;R,4,; R,5,;R,6,;R,7,;)</Contain> </ompartment> </ompartmentblok> <omplexblok Num="7"> <omplex j="1"> <Name>PIKFYVEVAC14FIG4</Name> <Position>( , , , )</Position> </omplex> </omplexblok> <physialentityblok Num="1"/> <proteinblok Num="15" /> <DnaBlok Num="1"/> <RnaBlok Num="1"/> <smallmoleuleblok Num="37"/> <reationblok Num="9"> <reation j="1"> <Name>PI(34)P2 is dephosphorylated to PI3P by INPP4AB at the early endosome membrane</name> <Type>T</Type> <Position>( , , , )</Position> </reation> </reationblok > <edgeblok Num="41"> <edge j="0"> <Name>A</Name> <Ends>(P, 1, R, 1)</Ends> </edge> </edgeblok> </Pathway> - 8 -

9 The first line is about the standard xml tag. The formal pathway is a hierarhial struture. The first type is ompartment. Compartment has attributes with Name, Position, Contain. The position is a string with the ombine of x, y, w, h of this ompartment. For the Contain, it is onsisted of all the biomoleules of the ompartment. Whih is splitted by ;. For eah biomoleule, it begins with its type, and id. The id is the index of this type. In PathBubble, it has 6 types. C for omplex; P for protein; D for Dna; Rna for Rna; E for PhysialEntity ; S for small moleule; R for reation For eah biomoleule, it has its id for j attribute. Its Name, its Type At the end of the file is about the edges, whih tells you the Name of the edge and Its two endpoints. The endpoints is begins with the type of Biomoleule and the id of biomoleule, and ends with the type of Biomoleule and the id of biomoleule Supporting Pathway ortholog gene data format You an upload you own gene data for ortholog analysis in PathBubbles. Below we will you show the gene data format, whih is tab-delimited format. The first olumn is about the symbol of gene, and the seond olumn is about the gene orthologous relationship between this speies and human, whih is if this gene an be found in human pathway, it is the Reatome human database identifiation number or if this gene an t be found any human pathway, it is the \N tag. Table 2 orthologous relationship of the input data between two speies symbol dbid ADA \N CDH AKT MED NR2E Supporting Pathway gene expression data format You an upload you own gene expression data for expression analysis in PathBubbles. Below we will show you the gene data format, whih is a tab-delimited format. The first olumn is about the Entrez gene identifiation number, the seond olumn is about - 9 -

10 the gene symbol and the third olumn is about the ratio of the expression level of this gene between two biologial states. Table 2 gene expression of the experimental data between two biologial states gene_id symbol ratio SMAD SMAD SMAD SMAD9 Infinity SMAD SMAD SMAD TGFBR TGFBR SHC SHC4 Infinity SHC3 NaN SHC GRB SOS SOS Introdution of PathRings Data Analysis PathRings integrates all the existing pathways of Reatome (1417) in a single Sunburst visualization, and uses olor to map interesting information, whih is onvenient to ompare, query and validate hypothesis. In PathRings, you an view eah biologial pathway network in a single Bubble. You an find ross-talking relationship between different pathways, you an ompare the ortholog information between different speies. You an upload your own experimental data (gene expression data) to ompare the result between different pathways, and figure out the detailed onnet protein information by the Table view Cross-talking Information When you open a TreeRing, it will show you all the pathway names of the First Level of the TreeRing in the enter. If you want to see the ross-talking relationship between pathways, you an lik the M on the Menu Bar, and then, you should selet Show CrossTalk option instead of the default Show Pathway Name option in the first dropdown menu.(see Figure 8 () ) The rosstalking information showed in the graph represents the relationship between pathway in a same level. You an hange the ross talking level by seleting the rosstalklevel dropdown menu. You an right lik the red bar to lookup the detailed ross-talking protein information. You an lik the ross-talking ell of a gene(see Figure 8 (d) ) in the table to see the ross-talking pathways, whih will be highlight in the parent-tree ring using yellow dots.(see Figure 8 (b) )

11 a b d Figure 8. (a) Tree Ring visualization, (b) Sub-tree ring visualization, yellow dots attempt to represent the ross-talking pathways () Menu of tree ring visualization (d) Table ontains ross-talking proteins Ortholog Analysis Our pathway is from Reatome, whih is a database about human pathway. We an use the pathways of human to predit all the pathways of other speies by providing their gene orthologous relationships between two speies, so that we an know the pathway relationship between speies. There are three types of relationships between a speie and human, Complete, Partial, Empty. Complete: If all the gene of a speies an be found in a pathway of human, we all this pathway is Complete to a speies. Partial: If just some gene of a speies an be found in a pathway of human, we all this pathway is Partial to a speies. Partial: If all the gene of a speies an not be found in a pathway of human, we all this pathway is Empty to a speies. In PathRings, all the three relationships of a pathway are enoded by olor. ( Yellow for Partial, Green for Complete, and Purple for Empty ). When you open a TreeRing, the default view will show you the ortholog relationship between Gallus and Human (see Figure 9 (g)). In the right orner of the Bubble, it will show you the olor sale bar with 3 types of ortholog relationship (see Figure 9 (f)). And also you an view ross-talking information relationship by hanging Show Pathway Name (see Figure 9 (b)). You an hange the default speies by seleting Choose Speies menu. You an upload your own gene data of a speies by seleting your own gene file and loading it

12 g a f b d e Figure 9 Orthologous analysis If you want to see the detailed orthologous genes of a pathway between two speies, you an right lik a red bar on the ring. (see Figure 9) It will give a Table Bubble (Figure 9 (d)), whih shows you the shared protein information of disease pathway between Human and Gallus. The Table is sortable, you an lik the header of the table to sort it. And also if you are about the detailed symbol protein information, you an right lik the interested symbol name Gene Expression Analysis PathRings provide gene expression analysis for a ertain speies. Gene Expression analysis is based on a ertain speies. So at first, you need to do the Ortholog Analysis (see the previous setion). And then you an unpload your own gene expression data (see the expression data format setion). You an input your ut-off of gene expression ratio, you an input your label for the up expressed and down expression bar. You an view the detailed expressed genes through table bubble. (Figure 10 (g)) You an obtain the gene information from the NCBI browser. (Figure 10(j))

13 a b (1) e d f (2)

14 h g i j (3) Figure 10 Gene expression analysis