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.