Tutorial

Query a driver gene

On the Portal or Search pages, enter a gene name into the search bar at the top of the screen. After a second or two, a report will be created for that gene, showing associated insertions, and highlighting datasets in which the gene is a common insertion site. Note that anywhere you see a "[?]" in the report, you can click for more information.

The page is accessed nearly anytime a link with gene name or locus identifier is clicked, or when a gene is queried from the main page.

	The search bar, in which you input your query gene.
	A summary containing annotations and external cross-references.
	An insertion map, which shows the insertions and insertion pattern across all of the tumor datasets.
	The frequencies in which the gene is altered in the different primary tumor models. Clicking on a bar will take you to a dataset page that highlights the driver genes in the corresponding dataset.
	The frequencies in table form. Clicking on the dataset will take you to a page for that specific dataset highighting the driver genes. Clicking on the insertion pattern navigates a page highlighting the insertions in a specific dataset.
	The frequencies in which the gene is altered in the datasets defined by biological properties. Clicking on a bar will take you to a dataset page that highlights the driver genes in the corresponding dataset.
	The genomic context around the query gene. Clicking on other gene loci will produce a report for that gene.

View the driver genes in a dataset

On the dataset page, enter a dataset name and a report type into the form at the top of the screen. Note that the report type is either "gene" or "driver", wherein the former considers all insertions in the analysis and the latter considers only high read depth insertion sites, which indicates insertions that are driving tumor development.

The page is accessed either through the welcome page (by selecting a dataset in the pie chart), or through the gene search page when selecting a dataset in the barcharts or cancer table.

	In the form, select the report type and the dataset name.
	A summary dataset annotations and a list of the most frequenty occurring common insertion site genes. Note that you can click the "transposon", "inducer", "sensitizer", "pathology", "organ", and "sex" tabs to get a breakdown of samples that correspond to the different types of these classes.
	A plot highlighting correlations between genes in tumors.
	A list of common insertion site genes in table form. Various statistics that can be used to rank the important of the genes are listed, such as p-value and average read depth. An alterative method was also applied to the dataset to determine common insertion sites, irrespective of gene boundaries, and if the gene overlaps with such a region that region is shown. Clicking on the genes or loci in this table will perform a query for that element on the Search page.
	A list of the tumors that compose the dataset, and some of their attributes. Note that if you click on the tumor name, you will navigate to a page that details the insertions in that tumor.

View an insertion pattern in a specific dataset

This page is accessed via links describing an insertion pattern ("activating", "inactivating", or "indeterminate") on the gene search and dataset pages.

Once you are on this page, you can change the dataset name and data type by altering the form at the top of the page.

	The search form, in which you specify the data type and the dataset to which the insertion data will be restricted.
	A summary containing annotations and external cross-references.
	An insertion map, which shows the insertions and insertion pattern in the selected tumor dataset.
	The genomic context around the query gene, considering only insertion densities in the selected dataset. Clicking on other gene loci will produce a report for that gene.
	The tumors containing insertions in the selected dataset and gene.

In depth view of insertions in a tumor

This page is accessed via tumor identifier links on the dataset and pattern pages. An example of this page can be viewed here.

	A summary highlighting a few properties of the tumor.
	Various insertion properties across the tumor, such as transposon reads across different chromosomes, locations, and in different orientations.

Example genome locus search

This functionality is accessible via the search page. An example of this page can be viewed here.