Pathway Explorer
The “PathLay - MAPS” page will be displayed after the configuration and the submitting of an analysis on an Experiment Package in your home. IDs coming from your datasets will be portrayed as different indicators on pathways depending on the Analysis Mode chosen (see more “Selecting an Analysis Mode”). This page allows you to:
Display your datasets on pathways
Filter pathways by selecting a specific gene/protein/miRNA/TF ID or by multiple IDs
Select a cellular compartment and display only the IDs localized in it
Select indicators and display their infos on the clipboard
Save indicators of interest and download them as a tab-separated text file
Filter pathways by selecting an “Agreement” between Gene/Proteins and Methylation, miRNAs or TFs
Warning
The “PathLay - MAPS” page is directly accessible after you hit the “Submit” button allowing you to navigate through pathways right away but depending on how much data PathLay needs to process, some indicators may not be displayed correctly from the go and require more time.
Highlighting Feature
In this sections two selectors are displayed and their content varies depending on the features enabled during configuration. The first selector lists the categories of components available between: Genes, Proteins, TFs, miRNAs, Methylations, Chromatin Statuses and Metabolites. Selecting one data type will switch to the respective component selector filled with the available IDs. When an ID is chosen, all the indicators related to it will be highlighted with a pink dotted border, and the maps not containing any indicator of interest will be disabled from the map selector.
Note
To reset the highlight simply select the first option from the ID selector.
Note
The highlight feature will highlight only those indicators currently available from the displayable maps. This means that when a query from the “Selectors” section has been performed, the selectors in the Highlight section will be filled only with the components represented on the maps that remained available after it.
The Clipboard
The Clipboard is a freely movable window that will be displayed as soon as the “Clipboard” writing is clicked in the menu. It is composed by two boxes, the “Info” box and the “Selected” box. The “Info” box will display the information related to a clicked indicator, this includes every ID that the indicator is portaying, with their differential expression values and other IDs eventually linked. Cliking on the IDs in the “Info” box will open up a page in the online database of reference for that data type:
NCBI for genes
UniProtKB for proteins
Mirtarbase for miRNAs
gsea-msigdb for TFs.
Once you have clicked an indicator on a pathway and its information is displayed on the Clipboard, you can click the “Add” button below the “Info” box and save the indicator inside the Clipboard’s “Selected” box. It will be listed as a smaller indicator under the name of the pathway from where the selction has been performed. Selecting this smaller indicator in the box will also display its information in the “Info” box and if the “Remove” button is clicked, the indicator will be removed from the “Selected” box. The “Select” button under the “Selected” box on the Clipboard performs the same operations as the highlight button in the Highlight Section, thus applying a dotted magenta border on the indicators of interest and disabling maps not containing them in the map selector. The last feature provided by the Clipboard is the “Download” button which allows to download a tab separated text document listing all the information regarding selected indicators currently populating the “Selected” box.
Note
Closing the Clipboard by clicking the “X” on the top right corner will not delete any selected indicator from the “Selected” box.
The Selectors Section
- This section contains the main query system of the “PathLay - MAPS” page allowing to perform a more sophisticate three level selection by:
IDs
Agreement between two components
Ontology (Cellular Compartments)
These selections can be performed by adding a query tag using one of the three selectors and clicking the respective “Add” button. Once all the query tags you are interested in are added to the pool on the right, the query can be performed by clicking the “Select” button.
- A brief summary of the rationale behind the query is the following:
The IDs provided are rounded up and only those maps that contains indicators representing them are allowed to proceed in the query. Is important to note that this step works with an “AND” approach so, whenever a map does not represent even one of the IDs provided, it is discarded and thus removed from the selector.
The Agreements provided are rounded up and the indicators that are currently displayable or that passed the previous step of the query, are checked for all the Agreements. Whenever an agreement is not satisfied, the indicator is hidden and if all the indicators in a specific map don’t satisfy the agreements, the map is discarded and removed from the selector.
The Ontologies provided are rounded up and the indicators that are currently displayable or that passed the previous step of the query, are checked for components that refers to the cellular compartments selected. Whenever an indicator doesn’t refer to one of the compartments selected, it is hidden and if all the indicators in a specific map don’t refer to the cellular compartments, the map is discarded and removed from the map selector.
To reset the interface to its default state simply click the “Reset” button next to it. Details on each type of query tag are provided below.
Select by IDs
The first row in the Logical Section is composed by a selector that allows the selection of a data type between “Gene”, “Protein”, TFs, “miRNA”, “Methylation”, “Chromatin” and “Metabolite”, depending on your analysis configuration. Selecting one data type will pop up another selector with a list of IDs of the data type chosen, in a similar fashion of the HighLight section. Once an ID is selected, it can be added to the query pool “IDs Selected”. Every ID added to the pool will be represented as a query tag and can be removed from the pool by clicking the “X” button on the right. IDs’ query tag have colors are assigned considering the data type:
Light blue for genes
Purple for proteins
Red for miRNAs
Yellow for Metabolites
Grey for TFs, Methylations and Chromatin Statuses
The “Select” button will perform a pathway selection using the pool content as criteria: considering a strictly ID based query, only those pathways portraying all the IDs in the pool will be displayed in the pathway selector and kept available.
Warning
It is possible that loaded pathways cannot satisfy the requirements for the selection made. In this case the pathway selector will become empty. Resetting the selection with the “Reset” button will restore the pathway selector at its default state.
Select by Agreement
The second row in the Logical Section is composed by a series of selectors that allows the setup of the so called “Agreement” which is a feature that lets you select two related data types and select what type of correlation you are interested in. The main data type can be selected with the first selector which provides a choice between “Gene” and “Protein”, and the second data type can be selected with the other selector which allows a choice between “Gene” or “Protein” (depending on your main data type of choice), “miRNA”, “Methylation” or “TF”. After the two data types are selected, the last step to do is to choose a “Positive Agreement” or a “Negative Agreement” with the last selector and hit the “Add” button. The configured agreement will be displayed in the “Agreements Selected” pool positioned under the “IDs Selected” pool. Once the select button is clicked, indicators that don’t satisfy the requirements of the agreement will be hidden, thus if a pathway doesn’t have visible indicators it will not be included in the pathway selector. Multiple agreements can be added to the pool to make the selection more stringent. How various agreements work is reported in the following table:
As an example, let’s suppose we want to examine only the indicators including a gene and a miRNA in a positive agreement: it is only necessary to select “Gene”, “miRNA” and “Positive” from the selectors provided in the Logical section. A positive agreement between a gene and a miRNA is based on a negative correlation, so the indicators highlighted will either have an up-regulated gene and a down-regulated miRNA or a down-regulated gene and an up-regulated miRNA. As a next step, we could also be looking at methylations: easily enough, agreement selections can be stacked so we could also select “Gene”, “Methylation”, “Positive” and highlight only those indicators that satisfy both the agreements. As before, to remove it the “X” button on the right or the “Reset” button must be clicked.
Settings
The settings section in the “PathLay - MAPS” page will be displayed when clicking the “Show Settings” button and allows to change some graphical parameters for the indicators like size and transparency values.
Transparency and Size
Transparency and size of the indicators can be increased and decreased with the “Transparency Up”,”Size Up” and “Transparency Down”,”Size Down” buttons respectively.
Screenshot
It is possible to take a shot of the currently displayed pathway by clicking the “Open as image (to save..)” button.
Warning
Depending on your browser compatibility this feature can behave differently.