Difference between revisions of "Marker Annotations"
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==Outline==
 
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In this tutorial, we will:
 
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#. Load a set of markers into the Markers component.
 
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#. Retrieve annotations from NCI's CGAP database.
 
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#. View a gene annotation page.
 
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#. View a BioCarta pathway diagram in the caBIO Pathways viewer.
 
  
 
==Overview==
 
==Overview==
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The Marker Annotations component retrieves two types of information for a group of genes.  It retrieves links to pages from the CGAP database at NCI containing textual information.  It also contains links to BioCarta pathway diagrams provided through NCI's caBIO data service.  For this tutorial, we will examine a group of genes selected in  the '''Hierarchical Clustering''' tutorial. 
 
  
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==Loading a set of markers==
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The Marker Annotations component enables the retrieval of biological annotation information for a collection of genes. For every gene, the following data can be retrieved:
  
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You must select and activate a group of markers (genes) in the Markers component. You can use for example the 84 markers selected in the hierarchical clustering example.  However, as it takes about 5 seconds to retrieve the annotations for each marker, you can also load or select a smaller set of markers.
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* Links to gene detail pages.
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* A set of pathways containing the gene.  
  
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* To load a previously saved set of markers, go to the Markers component and click the "Load Set" button.
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* The set previously obtained via hierarchical clustering is in the tutorial data file "cluster_tree_total_pearsons_84_markers.csv".
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All annotations are retrieved from remote servers maintained by the National Cancer Institute (NCI) [http://biodbnet.abcc.ncifcrf.gov/ bioDBnet resource of the Advanced Biomedical Computing Center] (NCI Frederick).
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* The desired marker set should be activated by checking its box in the '''Marker Sets''' component. Here is an example using the data from the [[Tutorial_-_Clustering|Hierarchical Clustering]] tutorial:
 
  
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==Submit Query==
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The Marker Annotations module will retrieve information for all markers that belong to activated marker sets, or, more precisely, for the genes corresponding to those markers:
  
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[[Image:Tutorial-Markers-ClusterTree84.png]]
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[[Image:MarkerAnnotations_Marker_set_activation.png]]
  
  
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==Retrieving selected annotations==
 
  
  
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* In the '''Marker Annotations''' component, select '''Retrieve Annotations'''.  A portion of the returned results are shown below:
 
  
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E.g., in the example shown above, information will be retrieved about the genes STAT3 and CEBPB.  Clicking the "Retrieve Annotations" button initiates the communication with the remote server:
  
  
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[[Image:T_MarkerAnnotations_ClusterTree2.png]]
 
  
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[[Image:MarkerAnnotations_Controls.png|{{ImageMaxWidth}}]]
  
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==Displaying annotations and pathway diagrams==
 
  
  
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* The links under the heading '''Gene''' can be clicked to display information from the CGAP database at the NCI:
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While the information is being retrieved, a progress bar will be shown.
  
  
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[[Image:MarkerAnnotations_ProgressBar.png]]
  
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[[Image:T_MarkerAnnotations_GenePage.png]]
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==Pathway and Gene Annotations==
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The "Annotations" tab presents a summary listing of the annotations retrieved from bioDBnet:
  
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[[Image:MarkerAnnotations_Results.png|{{ImageMaxWidth}}]]
  
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The '''Pathway''' links can be clicked to display BioCarta pathway diagrams provided through the NCI's caCORE/caBIO resource.  The graphical components are themselves clickable to provide further information.
 
  
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* Click a pathway link.
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The listing contains at least one row for each gene which annotation information is available for. If a gene is associated with more than one pathways, then one row for every pathway is listed (e.g., as is the case above for STAT3). Every row displays the marker (i.e., probeset) id, the corresponding gene name and the name of the associated pathway.  
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* Go to the caBIO Pathway viewer component. Below is displayed the pathway for the gene viewed above.
 
  
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Right-clicking on a gene name shows the following menu options.  Each will link to the named data source to display gene information in your browser:
  
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[[Image:T_MarkerAnnotations_h_ppara_Pathway.png]]
 
  
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[[Image:MarkerAnnotations_Gene_Menu.png]]
  
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==New Content==
 
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[[Image:Biocarta.png]]
 
  
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[[Image:CGAP_click_on_gene.png]]
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* '''Go to Entrez for ''gene name'''''
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* '''Go to CGAP for ''gene name'''''
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* '''Go to GeneCards for ''gene name'''''
  
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[[Image:CGAP_summary_page.png]]
 
  
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[[Image:CGI_expanded.png]]
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Right-clicking on a pathway brings up a popup menu offering the following options:
  
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[[Image:CGAP_summary_page_gene.png]]
 
  
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[[Image:CGI_expanded.png]]
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[[Image:MarkerAnnotations_Pathway_Menu.png]]
  
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[[Image:CGI_disease_dropdown.png]]
 
  
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[[Image:CGI_summary_page.png]]
 
  
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[[Image:Data_source_checkboxes.png]]
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* '''View Diagram''': available only for BioCarta pathways. geWorkbench generates a diagram of the pathway based on the BioCarta description. Selecting the "View Diagram" option will display this diagram within the "Pathway" tab.
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* '''View Diagram on BioCarta site''' - View the BioCarta diagram in your browser directly on the BioCarta website.
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* '''Add pathway genes to set''': extracts the pathway genes for which there are associated probes in the microarray set currently selected by the user and places all such probes in a new marker set within the "Markers" component (by default, the marker set is named after the pathway).
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* '''Export genes to CSV''': creates a new text file containing a listing of all pathway genes. The file format (csv = comma separated values) is compatible with Microsoft Excel.  
  
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[[Image:Data source checkboxes.png]]
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The export file contains the following columns:
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* Marker
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* Gene
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* Entrez GeneId
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* Pathway
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* Entrez URL
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* CGAP URL
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* GeneCards URL
  
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[[Image:NCI_thesaurus_disease_big.png]]
 
  
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[[Image:NCI_thesaurus_disease_small.png]]
 
  
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[[Image:Pubmed.png]]
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[[Image:MarkerAnnotations_h_erkPathway.png]]
  
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[[Image:Select_marker_sets.png]]
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A BioCarta pathway image is displayed above after selecting the "View Diagram" option from the "Annotations" tab.
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* '''pathway dropdown box''' - The drop-down box, on the top left corner above the diagram, shows the name of the currently displayed diagram. The component keeps a history of all BioCarta diagrams selected by the user; using the drop-down it is possible to switch among the corresponding pathway images.
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* '''Clear Diagram''' - this button clears the currently displayed diagram.
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* '''Clear History''' - this button clears the currently displayed diagram and removes all pathway history information from the pathway name drop-down box.
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* '''Image Snapshot''' - save a snapshot of the diagram to the [[Workspace]].
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==References==
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Mudunuri,U., Che,A., Yi,M. and Stephens,R.M. (2009) bioDBnet: the biological database network. Bioinformatics, 25, 555-556. [http://www.ncbi.nlm.nih.gov/pubmed/19129209 link to paper]
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[http://www.biocarta.com BioCarta]
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[http://www.biocarta.com/legal/terms.asp Biocarta Terms of Use]

Latest revision as of 18:27, 22 January 2014

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Overview

The Marker Annotations component enables the retrieval of biological annotation information for a collection of genes. For every gene, the following data can be retrieved:

  • Links to gene detail pages.
  • A set of pathways containing the gene.


All annotations are retrieved from remote servers maintained by the National Cancer Institute (NCI) bioDBnet resource of the Advanced Biomedical Computing Center (NCI Frederick).

Submit Query

The Marker Annotations module will retrieve information for all markers that belong to activated marker sets, or, more precisely, for the genes corresponding to those markers:

MarkerAnnotations Marker set activation.png



E.g., in the example shown above, information will be retrieved about the genes STAT3 and CEBPB. Clicking the "Retrieve Annotations" button initiates the communication with the remote server:


MarkerAnnotations Controls.png


While the information is being retrieved, a progress bar will be shown.


MarkerAnnotations ProgressBar.png

Pathway and Gene Annotations

The "Annotations" tab presents a summary listing of the annotations retrieved from bioDBnet:

MarkerAnnotations Results.png


The listing contains at least one row for each gene which annotation information is available for. If a gene is associated with more than one pathways, then one row for every pathway is listed (e.g., as is the case above for STAT3). Every row displays the marker (i.e., probeset) id, the corresponding gene name and the name of the associated pathway.

Right-clicking on a gene name shows the following menu options. Each will link to the named data source to display gene information in your browser:


MarkerAnnotations Gene Menu.png


  • Go to Entrez for gene name
  • Go to CGAP for gene name
  • Go to GeneCards for gene name


Right-clicking on a pathway brings up a popup menu offering the following options:


MarkerAnnotations Pathway Menu.png


  • View Diagram: available only for BioCarta pathways. geWorkbench generates a diagram of the pathway based on the BioCarta description. Selecting the "View Diagram" option will display this diagram within the "Pathway" tab.
  • View Diagram on BioCarta site - View the BioCarta diagram in your browser directly on the BioCarta website.
  • Add pathway genes to set: extracts the pathway genes for which there are associated probes in the microarray set currently selected by the user and places all such probes in a new marker set within the "Markers" component (by default, the marker set is named after the pathway).
  • Export genes to CSV: creates a new text file containing a listing of all pathway genes. The file format (csv = comma separated values) is compatible with Microsoft Excel.

The export file contains the following columns:

  • Marker
  • Gene
  • Entrez GeneId
  • Pathway
  • Entrez URL
  • CGAP URL
  • GeneCards URL


MarkerAnnotations h erkPathway.png


A BioCarta pathway image is displayed above after selecting the "View Diagram" option from the "Annotations" tab.

  • pathway dropdown box - The drop-down box, on the top left corner above the diagram, shows the name of the currently displayed diagram. The component keeps a history of all BioCarta diagrams selected by the user; using the drop-down it is possible to switch among the corresponding pathway images.
  • Clear Diagram - this button clears the currently displayed diagram.
  • Clear History - this button clears the currently displayed diagram and removes all pathway history information from the pathway name drop-down box.
  • Image Snapshot - save a snapshot of the diagram to the Workspace.

References

Mudunuri,U., Che,A., Yi,M. and Stephens,R.M. (2009) bioDBnet: the biological database network. Bioinformatics, 25, 555-556. link to paper


BioCarta

Biocarta Terms of Use

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