Report Page Tour

This page will give a brief tour of the updated Interactive Pathway Diagram Report pages.  We'll begin at the top of the page and work our way down, or you can jump to your section of interest using these links:

Jump to information about the:
Description Section
Pathway Diagram Section
Go To Section
Genes in Pathway Section
Additional Elements Section (see also the Go To Section)
Disease Annotations to Pathway Genes Section (see also the Go To Section)
Pathway Annotations to Pathway Genes Section (see also the Go To Section)
References Section (see also the Go To Section)
Ontology Path Diagram Section (see also the Go To Section)
Import into Pathway Studio Option

 
Interactive Pathway Diagram Description Section

 


The Description section has the title of the pathway with the Pathway Ontology term in parentheses and a link to the Ontology Report page for the term along with the description itself which in expandable format. By clicking on ‘(more)’ one gets to the full description; clicking on ‘(less)” brings the description to the default short format (thick arrows). At the end of the description paragraph there are links to associated or related GO term, entries at KEGG and Reactome databases, as applicable. Protein domains mentioned in the description have links to their entries in the Pfam database (all, thin arrows).

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Pathway Diagram Section
Diagrams are being created using the Ariadne Genomics Pathway Studio software package, currently version 8.0. The package comes with the mammalian ResNet Database various types of data on rat, mouse and human genes, diseases, small molecules, treatments, etc. When the diagram is saved as HTML, a folder is created with files for every object in the diagram. When the files are loaded on RGD’s website, a parser looks for particular properties such as RGD:ID that makes the gene objects linkable to their gene report page(s).
Additional properties can be created in ResNet; this feature has been used to add the Pathway Ontology ID or a pointer to external links.  These properties are also parsed; their values makes it possible to link to ontology report pages for other pathways present in diagram, to PubChem or ChEBI entries for small molecules or to lists of genes for members of a class or a complex. Shapes relate to particular functionalities, e.g., kinase, phosphatase, transcription factor, etc.

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'Go To' Section
In this section, entries which could be accessed by scrolling down the diagram report page are listed in tabular form. Clicking on any of them, will take the user directly to their position on the report page. Currently these entries are: Genes, Additional Elements, Disease annotations to Pathway Genes, Pathway annotations to Pathway Genes, Ontology path Diagram. As a note, if there is an altered version of a pathway with annotations and/or diagram available that entry is also listed in the Go To table (not applicable in the example given). As the Pathway Project continues to develop, more entry aspects will be added, such as for instance the pathway suite(s) or pathway suite network(s) the pathway may be associated with. The individual entries are explained in more detail in the sections devoted to them.

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Genes in Pathways Section
The list of gene annotated to the pathway term are provided by species, in a tabular form that can be sorted by several criteria (thin arrow). The default is the set of rat genes with choices for the mouse and human genes (thick arrow). The table provides links to the GBrowse tool for the rat and human genes [for more on GBrowse see the help page available here] and the references used in the annotation process along with information on the chromosome, start and stop positions. The ‘A’ icon at the far right end of an entry, stands for ‘Annotations’ and provides a link to a page with all the annotations for that gene across all ontologies RGD is using. Note that one can select to see annotations to the term and the term’s descendants or only to the term by selecting or deselecting the box ‘show annotations for term’s descendants’, respectively (thin arrow). Clicking on the icon tree to the right of the pathway’s name (circled), here ‘interleukin-1 signaling pathway’ brings up the tree view of the term in the ontology from the ontology report page

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Additional Elements in Pathway section
Elements such as other pathways, small molecules, gene groups, complexes or functional classes present in the diagram are listed with a small description and as applicable, links. While the links are also available from the diagram itself, the separate listing provides an additional means to access them while offering a brief description without the need to access the page. Objects representing the same gene but differentiated functionally or via location can easily be distinguished. In the example provided: ‘diss-Irak1’ is Irak1 gene product that has dissociated from the receptor complex, ‘cytTraf6’ is the Traf6 gene product which has translocated to the cytoplasm, both events are important for the unfolding of interleukin-1 signaling pathway (arrows).

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Disease Annotations to Pathway Genes
The disease annotations that have been made for the rat genes in the pathway are listed in a tabular format that can toggle between the default view with the diseases alphabetically listed in the left column and the genes in the right column, (left image). By clicking on the Genes/Disease tab on top, a new table is offered with the genes in the pathway alphabetically listed in the left column and in the right column all the disease annotations for those genes, separated by comas (right image). Clicking on a disease in any of the two tables, brings up the ontology report for that disease term.

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Pathway Annotations to Pathway Genes

Other pathway annotations that have been made for the rat genes in the pathway are listed in a tabular format that can toggle between the default view with the pathways alphabetically listed in the left column and the genes in the right column, (left image). By clicking on the Genes/Pathways tab on top, a new table is offered with the genes in the pathway alphabetically listed in the left column and in the right column all the pathway annotations for those genes, separated by comas (right image). Clicking on a pathway in any of the two tables, brings up the ontology report for that pathway term.

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References Section

The reference section of the pathway diagram report page lists all the PubMed references that have been associated with the pathway in RGD. By clicking on a reference brings up the reference report that provides links to PubMed. By clicking on the green plus sign will bring up the associated pathway or the annotated objects.

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Ontology Path Diagram Section
This part of the diagram report page shows the path(s) from the term to the root of the pathway ontology. Highlighted in a darker shade is the term itself. Clicking on it or any of term(s) above will bring up the ontology report page

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Import into Pathway Studio Option
The last element in the pathway diagram report page is the option of importing into the Pathway Studio tool the .gpp file for users that have the Ariadne package.
The option is right under the Ontology Path Diagram; mousing over the file – here  ‘interleukin-1signaling pathway.gpp’, and clicking, will bring up a selection window with the option of opening the file with Pathway Studio or saving it.

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