Table of Contents
- General Information
- Cytoscape Web Controls
- Selecting a node/edge
- First neighborhood
- Changing layout
- Interaction information
- Protein/Interaction Search
- Second neighborhood
The start page of HINT-KB2. By clicking on the links appearing on the left, you can browse information about Protein-Protein Interactions, Complexes and Functions. Furthermore, you can create your own datasets, read about the Web API, find relative links or contact us. Each one of the tools provided is explained further in the following paragraphs.
In addition, there are some icons that appear in every page. Their functionality is described
- : The user can create a new account or sign in HINT-KB2. In case the user has signed in, their profile information are displayed. In addition, the user can view/change their profile information by clicking on the button, or change their password by clicking on the button.
- : Shows the statistics of the data contained in our database.
- : Redirects the user to the homepage of HINT-KB2.
- : Redirects the user to the Biotools page, where they can access two other tools of our laboratory: ncRNAclass and Superclusteroid.
Positive Interactions Search
This page shows protein-protein interactions that are classified as positive using the 0.075 threshold. The user can specify their own threshold for the classification of the interactions, by changing the value appearing in the threshold value field. After specifying a threshold, the user can see the corresponding positive interactions by clicking on the button. Furthermore, feature normalization can be applied, by checking the option:
- By pointing on the column titles, the user can see information regarding the corresponding column:
- The user can click on under the co-expressions column, in order to show the co-expression values for the corresponding interaction.
- By clicking on the button, one can download the positive interaction results in a csv file where the values are separated with tabs. Note: The process of creating the file to download might take from 30 seconds up to 3 minutes.
Negative Interactions SearchPlease check the Positive Interactions Search section above.
Search by Protein
In this page, the user can search for a protein of their choice and see information about its interactions with other proteins, clusters that contain it and functions by which the corresponding protein is characterized. Furthermore the user can see the visualization of the protein interaction network of the specified protein. In order to get help on the visualization part, please check the PPI Network Visualization section.
- When the user enters two or more characters in the search field, a list of Uniprot IDs containing those characters appears:
- Feature normalization can be applied to the results (please check Positive Interactions Search section.)
- Protein's PPIs: The specified protein's interactions are shown. For more information concerning this tab, please refer to the Positive Interactions Search section. Note that in this tab, no threshold is used, so all the protein's interactions are diplayed.
- Protein's PPIs Visualization: The visualization of the protein's positive interactions network. More information concerning the visualization tab can be found in the PPI Network Visualization section. Note: By switching among the tabs, the network visualization will be re-initialized, so the result might look a bit different.
- Protein's Clusters: Displays the clusters that contain the specified protein. The user can click on a cluster of his choice in order to be redirected to the cluster's information page. For more information regarding the cluster page, please refer to the EEMC Clusters section.
- Protein's Functions: A list of the functions which characterize the specified protein. The list is ordered by the function namespace.
This page contains a list of all the clusters found by applying the EEMC clustering algorithm. The user can see additional information about a cluster, by clicking the button. When clicked, the button redirects the user to the corresponding cluster's page, where the proteins composing the cluster and the function that characterizes the cluster are displayed. The user can return to the cluster list by clicking the corresponding button appearing in the page of each cluster.
Furthermore, the user can download a txt file containing all the clusters, as well as the corresponding proteins and functions for each one. The download button can be found at the bottom of the EEMC Clusters page.
Search FunctionsThe user can search a function by entering the corresponding GO Term in the search field. By typing two or more digits, a list of relevant GO Terms appears. When the desired GO Term has been typed, the user can click the button in order to see the results. After the search, three tabs are created:
- Function : Displays information about the specified function.
- Complexes : Displays the clusters characterized by the specific function. The user can click on the cluster IDs in order to see information about the corresponding cluster.
- Proteins : Displays a list of the proteins characterized by the specific function.
This page allows an authenticated user to manage their datasets:
The user can View, Download or Delete any of their datasets, by clicking on the corresponding button.
Create a dataset
By using this tool, the user can create their own datasets. They can choose the number of positive and negative protein interactions they want
to include in their dataset. In addition, they can apply feature normalization to the results by checking the option:
Users can also choose if they want to include just HPRD positive interactions in the resulting dataset:
Finally, an authenticated user can save their dataset by clicking on the button. The saved datasets are displayed in "My Datasets" page.
For information concerning the resulting data, please refer to the Positive Interactions Search section.
The user can use some of the Representational State Transfer (REST) Services. These services are useful for third party systems that want to integrate the HINT-KB2 functionality.
The user can click on any link at the top of the page in order to see the corresponding service. There is a description for each service, its parameters, the values it returns and examples of using the service.
Web API ClientHINT-KB2 also offers standalone applications so the user can request data. The user can install the application to their computer and use the Web Services the website offers. The steps for installing the applications are described in the page.
LinksThis page provides the user with useful links of Human Protein Interaction Databases and databases containing Protein Interaction Annotation Information. By clicking on a link, a new window to the corresponding database will open.
Contact UsThis page provides the user with our contact information. In addition one can send their comments by using the corresponding form.
PPI Network Visualization
The selected protein is shown in red.
The user can move the nodes around by clicking on them and draging them.
The edge width is based on the confidence score. (greater width means larger score)
Cytoscape Web Controls
- : Allows the user to pan/navigate to the left or right of the visualization.
- : Allows the user to pan/navigate up or down in the visualization.
- : The user can click this option in order to drag and hold the visualization to navigate.
- : Zoom out or in the network.
- : Fits the network into the visualization screen (default zoom).
- : Allows the user to drag and hold in order to specify the zoom level of their choice.
Selecting a node/edgeBy selecting a node or edge, information will be shown in the Graph Information field. When a node is selected, the protein's Uniprot ID is shown. When an edge is selected, the user can see the interacting proteins' Uniprot IDs and the confidence score of their interaction.
First neighborhoodOne can see the first neighborhood of a node by right-clicking on it and choosing "Show First neighbors". The first neighbors and their confidence scores will be shown in the Graph Information field.
Another way of seeing a node's neighbors is by using the Decrease opacity on click option. It can be found
at the bottom of the page:
By enabling this option, whenever the user points over a node, every node's opacity is decreased, except for the specific node's neighbors.
Note: Having this option enabled might cause slower Flash response for large networks.
Changing layoutThe user can change the graph layout:
Force Directed: The confidence scores act as forces between proteins. Proteins with a large number of
interactions come closer, while proteins with a small number of interactions drift away from the graph center.
Radial: The graph is drawn by using the selected protein as the center and the rest of the proteins
are placed in circles based on their distance (hops) from the center.
Circle: All the nodes are placed in a circle.
By pointing on an edge, a tooltip showing the interacting proteins as well as the confidence score will pop up:
Protein/Interaction SearchThe user can search for a protein or an interaction by entering the Uniprot ID(s) of the protein(s) of their choice.
- Protein Search: The Uniprot ID(s), separated by commas, are specified in the corresponding search field.
If a protein is found, it is highlighted in blue.
- Interaction Search: Again, the user should specify the Uniprot IDs of his choice, separated by commas.
Every found interaction between the specified proteins will be highlighted in blue:
Second neighborhoodBy clicking on the button, the user can see the second neighborhood (2 hops away) of the selected protein. The interactions between the second neighborhood of the selected protein are not shown.
Respectively, when the user is seeing the second neighborhood, they can click on the button, in order to see the first neighborhood of the selected protein.