walkthrough

####Choosing a Starting Sample

The first step to using HitWalker2 is to choose a subject, a cell line in this context. Subjects can be referred to by name or alias (if added to database). Each subject is associated with multiple samples, one for each data-type and which may or may not have the same name as the subject. Below we choose the HEPG2_LIVER cell line by typing its alias Hep G2 name into the search box. After choosing the sample, HitWalker2 displays the relationships between the subject and its samples. At this point, if multiple samples are present for a given data-type, the appropriate one can be chosen. Note that these samples are only used to retrieve the data-types for the prioritization step for this subject.

####Adjusting parameters

Before carrying out prioritization or querying, it is possible to adjust the query or hit choice criteria or the parameters of the prioritization algorithm by clicking on the Adjust button and choosing the category of parameters to adjust.

####Prioritization

After the adjusting any desired parameters, the variants for the HEPG2_LIVER cell line can be prioritized relative to the gene targets of the drug assay results. To do this click the Prioritize button. After 10-30 seconds a table summarizing the prioritization results is displayed as is shown below.

Several options currently exist to explore the results after the table is perused online.

• Download the results table as a CSV which can be imported into Excel.

• Choose genes which will form the basis of visualization and querying.

Clicking Submit will bring the user to the visualization panel screen and display the connections between the selected genes.

####Anatomy of the panel view

Legend

1. Nodes

• Hierarchical collections represented as circles within circles
• There are 3 main types of nodes currently implemented:
  • Genes--Collection of Hits, Queries and Overlays
    • Hits are differentiated by whether they were/weren't seen to be a hit
  • Samples--Collection of subject/sample attributes such as gender or phenotypes
  • MetaNodes--Represents a collection of genes or samples
    • Not specifically represented in the legend

2. Edges

• Indicate the type of relationship(s) between the nodes

3. Panel
4. Panel Description

####Panel Interaction

Each panel can be interacted with using the mouse.