User Manual

For new functions in V5.0 only   For new functions in V4.0 only   For new functions in V3.5 only   For new functions in V3.0 only

Note: Functions shown with Italic style are only available to the registered users, and registration is free.

Requirements for Using VisANT

VisANT is implemented as a java applet which can be run in most common browsers and has been test with Chrome, FireFox, Safari and Internet Explorer on different platforms. JRE (Java Run-Time Environment) is required to run the VisANT and can be download freely:

Download Java

Note: VisANT is developed based on JDK 1.4, therefore can be run on any JRE in general.

Note: Many Linux distributions have OpenJDK as the default version of Java. For running VisANT, we recommend Oracle Java. Although they are very close, the Oracle version has better performance and contains fewer bugs.

Note: Recent development of Oracle Java have made Java Applet hard to run. The detailed instruction to run VisANT applet can be found below:

Instructions to run VisANT Applet

Overview

Start VisANT is easy, just visit http://visant.bu.edu/ and click start button as shown in the following figure (leave it as for historical memory :D):

Once the start button is clicked, the VisANT main window will pop out as shown as following (Clicking on each component in following window will bring you to the description of corresponding function):

As can be seen from above figure, VisANT is separated into two panels: the left one is the control panel, the right one is the graph panel which is used to construct the interactome network. Click on the buttons/menu in above figure to view the detailed description of the corresponding functions.

When VisANT starts, it loads the protein "ACS1" and its available interactome data as the starting point. The red color of "ACS1" indicates that it has been mapped to at lease one KEGG pathways, as the fact, if you mouse over the node, you will found that it has been mapped to four KEGG pathways as shown in following figure:

The node "ACS1" is just used as the starting point for inexperienced users of VisANT, it can be easily removed by clicking on the "Clear" button that will remove all nodes and edges in the graph panel.

Quick Tips

Mouse Manipulation at the Graph Panel

  1. Right single mouse clicking will invoke the pop-out menu.

  2. Left single mouse click will select the node/edge.

  3. Double click a node will expand the node, and double click it again will suppress the node's links.

  4. Move the mouse over the node/edge will show the annotation information of the node/edge as shown in the above figure.

  5. Mouse dragging, There are three buttons in the control panel that affect the function of mouse dragging as shown in the following figure:

When in the selection mode, dragging the mouse will draw a rectangular and all nodes within the rectangular will be selected; in the zoom-in mode, dragging the mouse will also draw a rectangular, and the graph within the rectangular will be zoomed in; while in the pan mode, dragging the mouse will move the whole graph. Different modes can be switched by clicking on the three buttons as also shown in above figure.

Summary of Mouse Operations

         Mouse over the node/edge: show the specific information of the node/edge

         Single mouse-clicking

o        Single mouse clicking over the node/edge: single select/deselect the node/edge

o        SHIFT/CTRL + single mouse clicking: multiple selecting/deselecting of the nodes/edges

o        Clicking on the empty space: clear selection of the nodes and edges.

         Double mouse-clicking:

o        For simple node:

         Normal: show the interaction of the node, query the interactions if its interactions have not been queried against the database (given that the Database Online option under Files menu is selected)

         Special: If double-clicking attribute of the VisAnt tag is configured in the VisML, launch the specified URL in the browser.

o        For metanode: expand/collapse the metanode, unless the metanode contains no nodes in which nothing happens

         Mouse dragging:

o        Left mouse dragging:

         Start from an empty space: draw a rectangular, and select all nodes within it.

         Start from selected nodes/edges: move the nodes. If dropped over a metanode, will ask whether the selected nodes shall be contained by the metanode.

o        Right mouse dragging: pan (move) the network.

         Mouse scrolling: zoom in/out the network

Copy/Paste

VisANT supports mixed searching of multiple entries and VisANT supports loading user's own data. Due to the security limitation of Java Applet, VisANT can not directly file from user's local computer. However, copy/paste is supported with hot-key CTRL-C and CTRL-V.

Searching/Loading the Data

Note: It is very important to select the right species before you search /load the data. The current species is always shown at the control panel and by default the species is Saccharomyces cerevisiae.

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Search Strategy

When VisANT searches a node, it first search the existing network to see whether the node is already there, if it is, it simply select the node. Otherwise, it will ask VisANT server to look into the dictionary stored in the Predictome database. If an entry in the dictionary is found, the entry together with all its interaction data and its alias, KEGG mapping etc will be returned to VisANT. For this reason, sometime the searching will load an entry with expanded linkages, sometime it just results in a selected nodes in the network shown on the screen. If no entry is found for the searched object, a warning window will be poped out to tell the user that no entry is found.

VisAnt allows user to multiple simultaneous search of the Predictome database. The searchable terms include protein name, ORF ID, GI number and KEGG pathway ID etc. All searched entries are case insensitive.

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Searching the Protein/Gene

To search the protein/genes, simply input the name/ORF/GI number of the protein/gene. Multiple entries are allowed and can be separate either by ',' or space/tab. When the search hits the database, the result will be centered in the graph panel. Following figure shows the search results of "ste3, ste4 and ste5": The search box allows the copy/paste to speed up the input. There is no limit of the number of the searched entries except the space limit of the text field supported by Java.

Be aware that different species are specifies by a drop-down list as shown at the left-down corner in above figure, in this example, it is Yeast. Also the label has been turned on by selecting the check box at the left upper corner.

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Searching KEGG Pathway and Chemical Compounds

KEGG pathway can be searched in VisANT using the KEGG pathway ID. The search entry must started with "map" followed by KEGG ID. For example, following figure shows the searched KEGG map00770.

The small round rectangular in the above figure indicates another KEGG pathway and double-click will load the corresponding into the screen. All EC numbers in KEGG pathway have been translated into the protein names. Chemical compound can also be search using the term such as "c04039', however, it will not query against Predictome database if the compound is not shown in the screen.

Note: Only metabolic pathways are currently available in VisANT due to the fact that KEGG has not release the KGML for other pathways yet.

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Load Your Own Data

This function is only available after users login as we assume that users will store the data they enter. All corresponding field will be enabled after user's login. Each row of the data includes four columns which are either separated by space/tab or ','. The first is the starting node, the 2nd is the ending node; the 3rd is the direction of the interaction that must be an integer, with 0 indicates no direction, 1 from starting node to ending node, -1 from ending node to starting node. The 4th column is the method used to discover the interaction which must be one of the field in the class table that will be mentioned later. Only the first column is required. When the 3rd and 4th column are not supplied, the interaction is assumed has not direction with method "unknown". Copy/paste is allowed here and all nodes are put at the left-upper corner of the graph panel when the "Add" button is clicked. Users can then either use layout function or manual layout the network. Following figure shows an example to load user's own data.

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Method Based Data Loading

To facilitate the large scale analysis of interaction network, VisANT enables method-based quick load of large interaction data set. This function is only available to the registered user as it take more server processing time. Clicking on the "All" button will load all interaction data available in Predictome database for the method. The method table can be invoked either from stand menu (under View menu) or from pop-up menu in graph panel.

Following figure shows the interaction network of the method "Two hybrid test" with circular layout.

Navigation

VisANT has a sophisticated system that allows easy navigation and exploration of the interactome map.

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Node Manipulation

Node Color

The general node is represented using color GREEN while these nodes that is mapped to at least one KEGG pathways are represented using color RED. However, the color schema is still a temporal solution and is not customized. It is reserved for further development of VisANT.

Note: Whether a node is mapped to a KEGG pathway requires the node expansion, therefore it is unknown whether a node has pathway mapping until it is expanded.

Node Selection

Node can be selected by simply clicked over the node. Multiple nodes can be selected by dragging a rectangular over the interested nodes as shown in following example (more information about mouse manipulation):

Note: To select/deselect extra nodes while keeping those already selected, please hold the CTRL/SHIFT key down and click corresponding nodes.

Select Linked Nodes

To select all the nodes linked with a certain node, first select the node, then select the "Select Linked Nodes" menu as shown in the following figure:

Node Expansion/Suppressing

'+' of the node indicates that the node's linkages are suppressed and '-' indicates all linkages of the node have been shown.

VisANT uses reference counter to determine whether the node should be visible. A starting node is treated as the root node and have a base reference counter 1. Each visible edge will add 1 reference counter to both of the nodes connected by the edge. This implementation enables VisANT to create a network by expand the nodes and suppress the network by suppressing the nodes. Following figure shows an example.

Above network is rooted by the node YKL178C and sequentially expanded with the node YCOR040W, YDR224C, YPR041W, NIP1 and HUA2. If suppress the network with the reversed order of the nodes just mentioned, the network will be suppressed and only the node YKL178C will be visible.

Double-clicking over the node will expand the node to show all the interactomes the node has. If the node has not been queried against Predictome database, a request will be sent to application server to get the all interaction data of the node. If multiple nodes have been selected, then user can right-clicking over the selected nodes and select corresponding menu to expand them as shown in following figure:

As can be seen from the above figure, there are two menu items to expand the nodes. In this example, we use the menu "Expand Selected". This menu expand the nodes that have not been queried against Predictome database. The other menu "Forced Nodes Expansion" will expand the nodes not matter whether they have been queried against the databases. As VisAnt can store the graph of user's research while Predictome database is updated constantly, this function is very used to update the network created by the user before.

Forced Node Expansion

As interaction data are periodical updated in Predictome database, it is desirable to query the database to get more information, especially for the stored network. However, to improve the efficiency of the network manipulation, in general VisANT will not query against database once the node has been expanded. To force the VisANT get the updated interaction information for certain nodes, this function is provided that is under the node menu.

Node Removing

To remove the nodes, first select them, then select the "Remove Selected" under the "Nodes" menu (either pop-up or stand menu). Following figure shows the example using the pop-out menu:

Note: When using the pop-out menu, please first move the mouse over one of the selected node, then right click the mouse. The menu is context sensitive.

Node's Visual Properties

The node's visual properties, such as label, size etc, can be customized through the properties window that can be activated under the "Node" menu as shown in the following figure.

Above figures shows that the property window is separate into two parts, the upper half groups the properties of the node and the other focuses on the properties of the node label. The description filed is only used for node's quick tip.

Note: Modification of visual properties can be applied to a single node, or a set of the nodes as shown in above figure. When applied to a set of the nodes, some fields will be grayed out as they are only available for single node.

Note:   By default the size of the node and the label text of node are determined by VisANT (option of "Auto" as shown in above figure), which means that the node size will be changed when the network graph is zoomed out/in. However, once the size of the node is selected by the user through property window, the size of the node will be fixed regardless the zoom in/out, which is a design feature, not a bug. The "auto" option of the label text works in the way as following: If the node has only one alias, then that alias will be used as the label text. This feature is based on the assumption that in general gene/protein alias is more familiar to biologists. All alias will be listed in the drop-down list together with the ORF ID and the label can also be customized by the user.

Quick Tip of the Node

The quick of the node allows the user to quickly gain detailed annotation of node without sacrifice of  the briefness of the interaction network. An example is shown as following:

The structure of node's quick tip works in following way: it starts with node's ORF, and followed by those aliases if the node has. Annotation together with the customized description through the property window will then be presented. If the node is mapped to several KEGG pathways, all the pathways will be shown one by one as shown in above figure. If the pathway has been loaded into VisANT, the title of the pathway will be shown (pathway 00010 in above example). Finally, the quick tips tells the user how many interactions (links) the nodes has if it has been queried against Predictome database.

Note: Quick tip can be turned off by uncheck "Quick Tip" checkbox at the left-upper corner of VisANT's control panel.

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Edge Manipulation

Edge Color

Biological interaction is represented with edge in VisANT. Edge color is specified based on the method used to uncover the biological interaction. If the interaction is uncovered by several different methods, then the edge will be colored in segments with corresponding colors of the methods. Following figure shows an example:

Above example shows that that the interaction between ICL1(YER065C) and YIR031C is uncovered by two different computational method, Gene Fusion and Phylogenetic Pattern, as indicated by the quick tip of the edge. Edge color can be customized through the Method Table, simply clicking on the small color button will pop out the color chooser window as shown in follow picture:

Note: in general if the interaction is more reliable if there are more methods uncover it. However, this is just a trend as it also depend on the method. In above example, the interaction is reliable as ICL1 and YIR031C mapped to same KEGG pathway 00630.

Quick Tip of the Edge

When moving mouse near the edge, the quick tip of the edge will be shown as in above window. The construction of the tip for the edge is a little simpler than the one for the node. It first shows the ORFs of the nodes connected by the edge which is followed by the methods used to uncover the edge.

Note: Quick tip can be turned off by uncheck "Quick Tip" checkbox at the left-upper corner of VisANT's control panel.

Select the Edge

To select the edge, simple click on the edge. VisANT only allows single selection of the edge so far. In some cases, multiple selection of the edge does happens such as "Cycle Detection", and VisANT also provides the function to reverse the selection of the edges under the "Edit" Menu.

Hide the Edge

To hide the edge, select the edge to be hide, then select "Hide Link" under Edges menu, as shown as following:

Be aware that the edge is just hidden, it is not removed from the network. Therefore it you suppress the node ICL1 and then expand ICL1 again, the edge between ICL1 and MLS1 will be shown again.

Filter the Edge Based on the Methods

By default, VisANT will display all interactions a node has when it is expanded. However, it is desirable to filter out the node's interaction based on the method. To do so, open the method table and uncheck the checkbox of corresponding methods. Following figure shows a network with embedded layout before and after the method "Two hybrid test" is filtered out"

Note: If an edge is uncovered by more than one methods, the edge will disappear until all methods for this edge has been unchecked. In above example, some edges at the right side of the network has some edges uncovered by more than one methods and are therefore still visible.

Edge Direction

As the interaction network may be hybrid, it is necessary to define the rule when add two interaction uncovered by different methods. Following table list the description of the edge direction and the rule for addition.

Note: The real meaning of the edge direction depends on the data and the method used to uncover the data. For example, in regulatory network, the direction generally represents the "binding action", while in metabolic pathway, the direction simply indicates the direction of bio-chemical reaction.

Self Loop

Sometime there is a connection to the node itself, which in general is termed as self-loop in VisANT. VisANT applies special presentation as shown in following figure:

VisANT provides filters to detect the self-loops which can be found under the menu "Filters".

Note: the real meaning of the self-loop depends on the data and the method used to uncover the data. For example, if the self-loop is uncovered by Gene Fusion, then it indicates that the gene is fused in this species and separated into two different genes in other organism, while in regulatory network, self-loop represents the auto-regulation.

Edge Weight Visualization

         Visualize the edge weight using the color of the edge. This option is available under Option menu and can be coupled with the option to visualize the edge weight using edge thickness, as shown below:

as usual, this option, as well as customized color for max/min weight, can be saved in VisML, as the attribute of  the <Edges> tag. Following links allow you to try out this new feature in VisANT directly:

Using edge color only       Using both edge color and thickness       Using edge thickness only

 

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Graph Manipulation

Zoom out/in

For large scale network, it is necessary to zoom in/out to get both overall/detailed view of the network. The "Zoom Out" button enables quick zoom out of the huge network by simply clicking on the button. To zoom in the detail of the network, the user can dragging a rectangular over the interested region as shown in the following figure:

In addition, the "Zoom Back" button in the control panel allows unlimited zoom back of each steps of zoom activities and "Reset button" will enable user back to the default zoom state.

Pan the Graph

To move the whole graph, click on the "Pan" button in the control panel of VisANT, be aware that mouse handle in the graph panel will be change to a "hand", then drag the mouse to move the whole graph. See mouse manipulation for more detail.

Layout the Graph

It is important to layout the network of large scale. VisANT has implemented several layout algorithm for this purpose, in which three of the layouts use the dynamic iterations and requires user interaction to stop the layout process by press the stop button.

These three layout algorithm use the similar method and can be used to reveal the dense nodes of the network. Following figure shows the same network using different layout algorithms:

Align & Distribute

As shown in the following figure, the align & distribute is under menu Layout:

Following figure shows the difference between align left, center and right:

and following shows the different between align top, middle and bottom:

Note: Align is always based on the LAST selected node. You can always select multiple nodes by dragging the rectangular, then hold on CTRL key and click the node you want other nodes align to.

Following figure shows how "distribute" works:

Note: align & distribute only apply to the selected nodes.

 

 

Network Analysis

 

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Find Shortest Paths between Selected Nodes

To run this filter, please select at least two node. In case there are more than two nodes, the shortest paths of all possible pairs will be searched. Following figure shows an example to search for the shortest between node YNL128W and YOR212W. Once the nodes are selected and the filter is activated, VisANT will pop out a window for path-related filters as also shown in following figure. The search results will then shown in the results field and all paths (includes all nodes and edges) will be selected as shown below. Be aware that the algorithm implemented in VisANT for this filter enables exhaustive search of the shortest paths between nodes. The example below shows that there are two shortest paths from YNL128W to YOR212W with length three. Furthermore, the shortest path from node A to B and B to A maybe different for the hybrid network (both directional and unidirectional, see Edge Direction for detail), VisANT lists the shortest paths in both direction.

Each line in the results panel corresponding each path/cycle/loop, single mouse clicking in each line will select each corresponding path in the network. Multiple selection is enabled by holding down the CTRL/SHIFT key when clicking in each line in the results field. The drop-down list and "Do Calculation" button enables user perform related filters without leaving this window. The button "Clear Results" is used to clear the results filed and "Clear Selection" button will clear the selection of network in the graph panel. To select all the paths listed in the result panel, please click the "Show All Result" button. The "Help button will load this page.

Note: the algorithm only searches the visible edges. If an edge is hidden, the algorithm will simply ignore it.

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Find Cycles (Feedback Loops)

A cycle is a closed loop with each edge of the same direction or no direction. This filter does not require the selection of the nodes. However, in case that selection of the nodes has been made, the filter will only report those cycles that involve these nodes, that is to say, each cycle will at least includes one selected node. Following example shows the detected cycles with the same network as above example.

Be aware that this algorithm finds the cycle with any length>2. However, as we already noticed that regulatory network may have cycle with length=2 based on VisANT's annotation system, as shown in following figure:

The edge between YAP6 and ROX1 with double arrows actually represents the multi-component loop as shown at the left of above figure. For this reason, the algorithm will soon be modified to include the edge with double arrow as the cycle with length=2.

Note: the algorithm will find of all nodes that form all possible cycles, however, the results panel may not list all possible cycles.

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Find Feedforward Loops

This algorithm detects the feedforward loop (FFL) as shown in following figure:

The FFL shown in above figure starts with node YPR104C and ends with node GNP1 (the data is based on method M0042), be aware that this FFL contains cycle YAP6-YAP4. As also can be seen from above example, our definition of FFL does not have any limit of the numbers of intermediate regulators, which is in theory more general than many other definition. 

Note: This filter has not been finalized yet, please use it with caution.

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Filter out the Loop/Path

It is often to get the sense out of a single loop/path from the complicated network. VisANT has provided corresponding functions to complete the task. Following figures show an example:

The first step is to select the path by click the corresponding line in the result panel as shown in the following figure:

then select the menu "Reverse Selection" Menu as shown in the following figure:

The third steps is to remove the selected nodes and hide the selected edges (if the action to hide the selected edges does not work, try click the path at the results panel again, then reverse the edge selection and hide the reversed edges):

Now only the edges and nodes belong to the path/loop left on the screen as shown in the right-bottom corner of above figure. To clear show the path, please select the menu "Start Elegant Relaxing..." and a loop in above figure will be laid out as a "real loop" as shown in following figure:

Note: when performing loop/path detection, the results panel may be overloaded. As a result, you may not see those cycle/loop passing through the nodes you interested in. To fix the problem, you can select these nodes and perform the detection again. In this case, only those paths/loops that pass through the selected nodes will be shown in the result panel.

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Degree Distribution of the Network

This function is invoked by the menu item under the View menu. Node degree is represented by its visible interactions regardless weather it has been queried against the database. The distribution is calculated to see its fitness with power-law curve that is shown as the blue line. Once the network changes, the function need to be re-invoked in order to take account of the change. Following figure shows the degree distribution of fusion network for Yeast (the correlation represents how well the power-law fits the distribution):

 

Network Transform

 

Data Integration

Note: Most of the integration annotations are only available after a node is expanded, this is merely for the consideration of performance and efficiency.

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Integration of Interactome

VisANT is backed by Predictome that has been evolved into an interaction database that containing both putative and experimental interactome data. Interaction data have been collected from various data sources and categorized based on the methods used to created the data. Please refer to the method table for more information. To get the detailed information of each method, please click the "Ref " button in the window of method table. Also reference the session of Edge of this manual for the detailed description of how interactome is visually integrated.

VisANT provides a special filter to find out these interactions that are uncovered more than one methods as shown in the following figure:

Figure A in above shows the original interactome network, apply the filter (the menu shown in figure A) will select all the edges and nodes connected by these edges. By reversing the selection of both nodes and edges using the menu shown in figure B, and then remove the selected nodes under "Nodes" menu and "Hide Links" under "Edges" menu, they apply the Spring Embedded Relax layout will get the network shown in figure B, in which all edges are uncovered by at least two methods.

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Integration with Other Annotation

KEGG Pathway

Each protein/gene has the complete information of the mapping to the KEGG pathway. As mentioned in the Node session, nodes having KEGG pathway mapping will be shown in red color and all mapped KEGG pathway can be seen with node's quick tip. In addition, all corresponding KEGG maps can be loaded through the "Available Links" under the "Nodes" menu, as following example shows:

In above example, node YBL016W has been mapped to several KEGG pathways, including 04010 MAPK signaling pathway. Corresponding KEGG link can be activated through the menu as shown in the figure and corresponding nodes will be colored (Fus3 is the alias of YBL016w).

In addition, the whole KEGG pathway can be loaded into VisANT as part of the interaction network, which provides the seamless integration between interactome network and KEGG pathway. This function can be activated through the menu "Expand Pathway" as also shown in above figure. More detail can also be found at Searching KEGG Pathway.

COG Orthology

It is desirable to map interaction network from model organism to homo sapiens based on orthology. VisANT provides two filters to this purpose.

  1. "Suppress Nodes Do Not Have Homologs in Human". This filters looks COG database for the human orthology and suppress all nodes that do not have human orthology.

  2. "Select Nodes Having Human Ortholog". This filter selects all nodes that have the human orthology based on COG database.

Both filters will tell the user how many nodes that do not have human homology. Once the filter has been applied to the nodes, the quick tip of these nodes will display all the human orthology gene/proteins as shown in following figure. Furthermore, the NCBI links of these human orthology proteins/genes under the available links menu item as also shown in following picture.

Sequence Annotation

VisANT provides NCBI and KEGG GenomeNet links for the sequence annotation as can also be seen under node's "Available Links" menu in above figure.
 

Functional Annotation

For genes/proteins in species such as yeast, fly, worm etc., VisANT also provides the link to species-specific database such as SGD etc. for functional annotation. The link is under node's "Available Links" menu (above figure) after the node name is resolved or the node links are queried against the Predictome database. On the other hand, VisANT in general provides descriptive annotations available in Entrez Gene database.

 

Input/Output

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Import Network into VisANT

Interaction/Pathway/Network data with various formats can be directly imported into VisANT, either copy/paste (CTRL-C/CTRL-V) the data into Your Data Text Area in the ToolBox Panel in VisANT, or directly load them from a local file (for local application and web start only). Different formats are recognized by VisANT automatically, here is the list of supported format:

  • Edge List: Default text format for non-XML-based data

  • VisML :Default XML format, containing all the network information. Network stored as VisML format can be safely replayed as it was stored.

  • Expression : Expression matrix file, the first line must start with #!Expression. Optional parameter addNewNode to determine whether to abandon the nodes that are not in the current network, e.g. addNewNode=false.

  • Macro/Batch :The file format to store a list of commands for VisANT to carry out. The first line must start with #!batch commands

  • ID-Mapping :This file format is designed to allow user to add various database IDs, as well as alias and functional descriptions, to the nodes in a network, must start with #!ID Mapping

  • KGML: The KEGG Markup Language (KGML) is an exchange format of the KEGG graph objects, especially the KEGG pathway maps that are manually drawn and updated.

  • GML : Graph Markup Language, a common graph file format supported by several network software

  • PSI-MI : XML standard format for molecular interactions supported by molecular interaction databases

  • BioPAX: Biological PAthway eXchange, standard format for pathway information supported by multiple pathway databases

To ensure the performance, except for VisML, the Fine Arts option under Option Menu will be turned off when the total size of nodes and edges > 12000. You can, of course, turn this option back on if necessary.

KGML

  KGML Homepage    

One nice feature of KGML is that it keeps the visual properties. However, the name of the nodes will need to be resolved using the MetaGraph-->Resolve All Nodes Name menu (NOT  the Nodes-->Resolve Selected Nodes Name menu because there are many nodes hidden in collapsed metanode) when data integration is required, such as the case where expression data need to be mapped to the nodes. Here is a macro file illustrates the steps to use KEGG pathway for expression enrichment analysis. Click here to try out.

hsa04310 [ xml | graphics ] Wnt signaling pathway. Click the graphics will load the KGML of the pathway at http://www.genome.jp/kegg/xml/hsa/hsa04310.xml

Please contact VisANT@zlab.bu.edu if you find bugs.

Tip: a KEGG pathway can be easily loaded into VisANT if the searched term starts with the "map", such "map04110" where 04110 is the pathway id (cell cycle pathway), the pathway for the current species will be loaded into VisANT. VisANT supports many different ways to load KEGG pathway, which are detailed in our publication VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.

GML

 GML Homepage    

VisANT has primary support of GML. Here is a GML example file, it can be loaded into VisANT directly, here is the network looks like:

Here is a macro file that will loop through 5 GML files for animation purpose,  Click here to try out.

 

Note: per user request, VisANT renders the shape circle in GML with VBALL shape, as shown above.

Please contact VisANT@zlab.bu.edu if you find bugs, or you have suggestions/comments.

PSI-MI

 PSI-MI 1.0 Homepage   PSI-MI 2.5 Homepage 

The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The PSI-MI format is a data exchange format for protein-protein interactions.

VisANT supports importing of PSI-MI data file. Here are two sample files in the format PSI-MI 1.0:

psi_sample.xml   Load this file in VisANT    |   Ito_expand.xml    Load this file in VisANT

Here is a sample file of PSI-MI 2.5:

BIOGRID-GENE-113010-2.0.32.psi25.xml   Load this file in VisANT

Please contact VisANT@zlab.bu.edu if you find bugs.

Note: if the interaction involves two interactors that belong to the different organisms, it will be ignored in the current implementation.

BioPAX

BioPAX Homepage

BioPAX is a collaborative effort to create a data exchange format for biological pathway data. VisANT supports importing data file of BioPAX format, both Level 1 and Level 2.

Level 1:BioPAX Level 1 represents metabolic pathway information. Here are two sample files (so far our parser only supports BioPAX file with only one pathway, we are working on to enhance it) :

The right show the result of VisANT visualization of this short demo provided by BioPAX group, which involves two pathway steps: the first step invloves two small molecules for both reactors and products, which are grouped to indicate this situation. The biochemical reaction is catalyzed (activation) by protein glucokinase; while the 2nd step only involves one reactor and product, and is catalyzed by protein phosphoglucose. All the participants are grouped into one pathway group.

biopax-short-demo-pathway.owl 

 Load this file in VisANT  

The is a real pathway from BioCyc, which enable us to examine the VisANT visualization schema of BioPAX pathway. The detailed annotation of the comparison is shown in the right figure, click on the image to get the full-size one in a new window.

biopax-example-ecocyc-glycolysis.owl

 Load this file in VisANT

original pathway in BioCyc

We apply the graphic annotation similar to KEGG pathway. For a given bio-chemical reaction A ---> B, if a catalysis C is presented, then the reaction will look similar to A ---> C ---> B. Same rule has been applied to modulation.

The pathway's layout is based on their pathways steps using a top-down manner. If there are more than one reactors/products in one Biochemical reaction, they are grouped; if one of the reactors is also one of the products in the previous pathway step, it is duplicated and grouped separately. For example, for two given reactions: R1+R2 ---> P1+P2, and P1+R3 ---> P3, then R1 will be grouped with R2, and P1 will be grouped with P2, P1 is then duplicated and grouped with R3. Each modulation and catalysis is counted separately.

Level 2:BioPAX Level 2 expands BioPAX to cover molecular interactions which are compatible with PSI-MI format supported by VisANT. In addition, the featured invention of Meta-Network in VisANT makes it nature for us to support unique features of BioPAX Level 2, including Pathway Hierarchy and Black-Box pathway. In fact, VisANT is so far the only network software that is capable to support visualization of network hierarchy. However, because Level 2 has not been finalized yet, sample files are not available. We are contacting BioPAX group in an effort to get earlier release of sample files.

Please contact VisANT@zlab.bu.edu if you find bugs.

Edge List

See User Manual for more information

The simplest format for network in VisANT, can also be used to create new nodes (one node per line, such as ste4 below) and edges. Users can simply enter or copy/paste text in the Add textbox in VisANT's toolbox and click the Add button to add a list of edges/nodes. This simple format also supports creation of Meta-Node, and a sample is listed below:
YAL054C YLR153C 0 M0020
YAL054C YLR153C 0 M0031
YAL054C YLR049C 0 M0034
YAL054C YHL043W 0 M0046
YAL054C YNL189W 0 M0034
YAL054C YMR280C -1 M004
YAL054C YBR117C 0 M0046
YAL054C YDR216W -1 M004
YAL054C YBR046C 0 M0036
YAL054C YBR049C -1 M004
YAL054C YER061C 0 M0036
YAL054C YDR207C -1 M004
YAL054C YHR041C 0 M0034
YAL054C YKL112W -1 M004

ste4
#complex M4453
YAL054C YLR153C YLR049C YHL043W
#group xx2323
YAL054C YLR049C YHL043W
#group
YBR049C
YER061C
YHR041C
#group myGroup
YER061C
YDR207C
YHR041C

Copy/paste above sample data to the Add textbox and click the Add button, then do a circle layout with the Layout-->Circle* menu and then click the Fit to Page button, a metanetwork will be shown similar to the one shown below:

VisANT supports the weighted edge, and a complete line of a weighted edge includes 5 columns:

 

Node_1 Node_2 direction Method_id Weight

 

Here is an example:

 

YAL054C YDR207C 0 M0037 0.263304413189123

 

Above line represents a weighted binary interaction between node 1 (first column) and node 2 (second column). The integer in the third column represents the direction of the interaction, i.e., 0 signifies an undirected link, 1 indicates that the link has a direction from node 1 to node 2 (we support KEGG notation for edge type, try out number 0-9 to see different type of edge), and negative sign "-" indicates the direction is from node 2 to node 1. The forth column represents the method id as can be viewed from method table in VisANT. The user can also add their own method in VisANT. The last column indicates the weight of this edge.

 

If you forgot the format, simply export a network in the format of edge-list using the File-->Export as Tab-Delimited File-->All menu.

 

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Save the Image

As the unsigned on-line java applet, VisANT can not directly save the image as the local file, however, VisANT does provide the on-line image saving function which can be activated through the "Saving the Image" menu item either under "File" menu or under pop-out menu. When this function is activated, the network shown in the graph panel will be represented in a web page as shown in following figure:

The graph can then be saved to user's local disk.

Note: In the situation when the node is big, an error saying that "there are two many colors" may happen as the big node may contain too many color level for GIF image. If this happens, change the node size to make the node in the network more uniform will be helpful.

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Export the Network

This function export the current network into a tab-delimited format. There are three options, as shown in the following figure.

Note: Export Nodes only can be used as a starting-point to create ID-Mapping file.

On-Line Only

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Save the Result On-Line

To save the file, simply click on the "Save" button as shown in following figure and the network will be saved to VisANT server with the name shown in the "Available File" drop-down list.

To save to a file with the name different file name, please click on the "Save As" button also shown in above figure, and an window will be popped out to ask for your input of the new file name:

To avoid potential problem of the file name, VisANT does not allow some chars (such as space, please user underscore to replace the space char) as the file name. Once VisANT accepts the file name, it will put the name as the current selection of the drop-down list "Available Files".

Note: The file is stored in VisANT server through the network and will be available to the user whenever he/she logins VisANT, not matter where the user is. For this purpose, this function requires user registration so VisANT can have unique identity for each user. As the space is also limited in VisANT, by default each user can only store 10 files on-line, however, this number can be modified per user request and space availability. Please send email to VisANT administrator if you need more space.

Note: The global font size and the control related with the three checkboxes in the left-upper corner of the control panel. All other information, including the customized information such as edge color etc, is stored in the file.

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Open the File

To open the previous stored file, select the file from the "Available Files" drop-down list and click the "Open" button. Be aware that the graph panel will be first cleared before the file is loaded.

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Delete the File

To delete the file, first select the file from the "Available Files" drop-down list, then click the button "Delete".

Note: Once the file is delete, VisANT has no way to recover the file.

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Share the Data

To enhance the research communication, VisANT provides function to share the networks built with VisANT. To share the file to other users, please first select the file to be shared from "Available Files" drop-down list (which indicates that a file need to be created for the corresponding network you want to share), then click the "Share" button, a window will popped out with corresponding file name highlighted:

In above example, the file to be shared is "y2h_rakesh", to share the file, the only required input is the email addresses of the corresponding users, other two fields are optional and are designed for the user to provide more information about the file to be shared. With the inputs shown in above figure, an email will be sent to the corresponding email address after the "Ok" button is clicked. Following figure shows the corresponding email:

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Open Shared Network

Once the user is notified by the email about files shared in VisANT, he/she needs to login VisANT to open the file. If the user do not have an account yet, he/she can open an account right away, see free registration for more information about account creation. If the user already login the system, he/she needs to logout and then login again in order to see the latest file shared by other users. The following figure shows the file shared based on above example.

As can be seen from above figure, the file "y2h_rakesh" is shown in the drop-down list of ""Shared Files". To open the file, select it and click on the "Open" button.

Note: Once the shared file is opened, it will no long appear in the list of shared files. The user must save it as his/her own file in order to keep it.

Note: The file shared by the user is merely a point to the corresponding user, therefore any modification made before the file is opened by the shared user will be shown to the user, and of course if the file is removed by the user, then the shared user will not be able to open the shared the file.

User Registration and Login

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Registration

Most functions provided by VisANT do not required user registration except those that have to uniquely identify the user. Registration of VisANT is free and the only required information is the right email address. Once the user pass the registration, an email will be sent to user with the initial password randomly created the VisANT. The email will tells user the URL to change the password, or the user can change the password when he/she logins the VisANT.

Please click here to register, the registration is also available through the Registration button at VisANT's control panel.

Note: The password you provided is encoded in our database. The information you provided will be exclusively used for VisANT.

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Login/Logout

Login is simple, please click login button at the control panel of VisANT, a login window will be popped out as shown in following figure:

The login window also enables user to change the password as mentioned previously. If unfortunately the user forgets the password, VisANT can send the password to the user's email address.

One the user login VisANT, the login button will become logout button. Please logout VisANT when you finish your work to secure your personal data.

Note: after version 2.0, user name and passwd can be saved locally when you run VisANT as a local application so that you no long need to type-in passwd and user name each time. This option is not available for on-line login

Control Panel

The Control panel enables user to quickly access certain functions provided by VisANT. The overview of the control panel can be found at the session of Overview of this manual, here we list the description of each component in the control panel:

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Labels. This checkbox provides global control to turn on/off the label of the nodes. However, this setting will be overwritten by node's individual label setting. For more information about node label, please reference Node Visual Properties. The default value of this checkbox is off.

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Auto Fit. When this checkbox is selected, the network shown in the graph panel will always fit to the size of the panel. The default value of this checkbox is off.

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Quick Tip. This checkbox enables the quick tip of the node and edge when mouse over them. It's default value is on. See Quick Tip of the node and Quick Tip of the edge for more information.

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Help button. This button will invoke this manual.

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Select button: This button will make the mouse in the selection mode, see Mouse Manipulation for more information. When the mouse is in selection mode, this button is disabled, otherwise, it is enabled and clickable.

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Zoom In button. This button will make the mouse in the zoom-in mode, see Mouse Manipulation for more information. When the mouse is in zoom-in mode, this button is disabled, otherwise, it is enabled and clickable.

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Pan button. This button will make the mouse in the pan mode, see Mouse Manipulation for more information. When the mouse is in pan mode, this button is disabled, otherwise, it is enabled and clickable.

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Zoom Out button. Click on this button to zoom out the graph.

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Clear button. This button clears the graph panel, please use it with caution as VisANT currently do not have undo function.

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Zoom Back button. This button provides the function to recover the previous zoom state. It will only be enabled when the network is either zoomed in or out. VisANT provides unlimited zoom back. See Zoom for more information.

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Reset button. When the graph is zoomed in/out, this button will be enabled and clicking on this button will reset the size of the node to the one before the zoom action, and clear all zoom states so no zoom back will be available.

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Fit to Page button. This button fit the network to the size of the graph panel. If the graph is in the zoom state, this button will clear all zoom state, however, the size of the node will remain untouched.

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Search button. Click on this button will search the proteins/genes/compounds/pathways entered in the search field.

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Search field. This text area allows user to enter the multiple components to search against Predictome database.

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Species drop-down list. This drop-down list is used to indicate the current species and also allow user to change the species. Note: if the user change the species while the graph panel has not cleaned yet, the user will be warned that the network in the graph panel will be cleaned if the species is changed.

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Register button. This button allows user to register while using VisANT, see Registration for more detail.

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Login button. This button allows user to login/logout, see Login/Logout for more detail.

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Save As button. This button allows user to save the network into a new file, see Save the Network for more detail.

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Save button. This button allows user to save the network into the current file, see Save the Network for more detail.

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Delete button. This button allows user to delete the current file, see Delete the Saved Network for more detail.

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Open Button. This button open the current file listed in the Available File drop-down list. See Open Saved Network for more detail.

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Share button. This button allows user to share the current file, see Share the Saved Network for more detail.

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Available Files drop-down list. This drop-down list lists all the available files saved by the user, the visible file indicates the current/last saved file.

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Open button. This button open the file shared by other users, see Open Shared Network for more detail.

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Shared Files drop-down list. This drop-down list lists all files shared by other users if there is any.

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Add button. This button adds data in the your data field to the current network shown in the graph panel, see Load Your Own Data for more detail.

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Your Data field. This field allows user to add more data, see Load Your Own Data for more detail.

Menu

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Standard Menu

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File.

Save the Image. This menu allow user to save the network in the graph panel as an GIF image file, see Save the Image for more detail.

Exit. this menu will close the main window of VisANT applet. However, it actually only hides it and the window can be restored by click the "Start" button at VisANT page.

Database Online. Deselecting this checkbox will disable all database-query functions. For example, search function will only perform screen search if this option is deselected. This option is saved in visML.

 

Enable a list of recent opened network file up to 9 files under File menu. These files can be quickly invoked by key combination CTRL-0-8. . This function is not available when run VisANT as an Applet

 

VisANT now starts with a startup network. Users running VisANT as application/web start will be able to use their own startup network. Please note that the startup file may be updated by VisANT server in case there is certain modification of method table. To save your own startup network, simply type CTRL-U or invoke corresponding menu item under File menu. The default startup file is shown as following :. Load startup.

Complete off-line when run VisANT as a local application. The startup file enables VisANT to run offline because it contains all necessary information.

If for any reason the user can not save the network, we have implement an emergency function that will copy VisML to Add text box (if the network is bigger, the rest part of VisML may be copied to Search box). The user can then copy the VisML from one or two textbox to a local file and email the file to VisANT@zlab.bu.edu, and we will help you to fix the problem and recovered at least, if not whole, most of the network. This function can be invoked by CTRL-Y or corresponding menu as shown above.

 

 

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Edit

Reverse Selection: Reverse the selection of both nodes and edges.

Reverse Node Selection. Flip the node selection.

Reverse Edge Selection. Flip the edge selection.

Clear. Clear the graph panel.

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View

Methods Table. Invoke Method table in VisANT, see Method-Based Data Loading and Filter the Edge for more information.

Statistic Report. Shows the statistic report of the current network shown in the graph panel. Following figure shows an example.

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Filters

Suppress Nodes Do Not Have Homologs in Human. Search the COG database and suppress and select those nodes that have human orthology. See Orthology for more information.

Select Nodes Having Human Ortholog. Search the COG database and select those nodes that have human orthology. See Orthology for more information.

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Layout. See Layout the Graph for more information.

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Nodes.

This menu is context sensitive and is only enabled when a node is selected. See Node Manipulation for more information.

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Edges.

This menu is context sensitive and is only enabled when an edge is selected. See Edge Manipulation for more information.

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Help. This manual

This manual and easy upgrade of VisANT when run as local application. VisANT is under active development and upgrade is now only one mouse-click away. A new menu has been added under Help menu. When the user query the Predictome database (e.g., search a protein), VisANT checks the update automatically and an icon will be shown near the Help menu if update is available. The user can click the icon to upgrade. (Upgrade is only applicable for users who download and run VisANT locally, other users always run the latest version of VisANT.

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Pop-out Menu. It is basically provides same function as standard menu. See corresponding item in standard menu for more information.